PDB Full entry for 1D10 HEADER DNA 20-OCT-89 1D10 TITLE STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES. ADRIAMYCIN AND TITLE 2 DAUNOMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.A.FREDERICK,L.D.WILLIAMS,G.UGHETTO,G.A.VAN DER MAREL,J.H.VAN BOOM, AUTHOR 2 A.RICH,A.H.-J.WANG REVDAT 4 07-FEB-24 1D10 1 REMARK REVDAT 3 24-FEB-09 1D10 1 VERSN REVDAT 2 01-APR-03 1D10 1 JRNL REVDAT 1 15-OCT-90 1D10 0 JRNL AUTH C.A.FREDERICK,L.D.WILLIAMS,G.UGHETTO,G.A.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,A.RICH,A.H.WANG JRNL TITL STRUCTURAL COMPARISON OF ANTICANCER DRUG-DNA COMPLEXES: JRNL TITL 2 ADRIAMYCIN AND DAUNOMYCIN. JRNL REF BIOCHEMISTRY V. 29 2538 1990 JRNL REFN ISSN 0006-2960 JRNL PMID 2334681 JRNL DOI 10.1021/BI00462A016 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NUCLSQ REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 2731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 120 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 60 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BOND DISTANCE (A) : NULL ; NULL REMARK 3 SUGAR-BASE BOND ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BONDS DISTANCE (A) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION CONTACT (A) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 SUGAR-BASE BONDS (A**2) : NULL ; NULL REMARK 3 SUGAR-BASE ANGLES (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BONDS (A**2) : NULL ; NULL REMARK 3 PHOSPHATE BOND ANGLE, H-BOND (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D10 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 288.00 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.54000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.05500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.27000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.05500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.81000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.27000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.05500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.81000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.54000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 28.11000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 28.11000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 26.54000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A 1 C2' DC A 1 C1' 0.103 REMARK 500 DC A 1 O3' DC A 1 C3' -0.070 REMARK 500 DC A 1 N3 DC A 1 C4 0.065 REMARK 500 DG A 2 P DG A 2 O5' 0.076 REMARK 500 DG A 2 C2' DG A 2 C1' 0.116 REMARK 500 DG A 2 O4' DG A 2 C4' -0.073 REMARK 500 DG A 2 C5 DG A 2 N7 -0.042 REMARK 500 DG A 2 N7 DG A 2 C8 0.040 REMARK 500 DG A 2 C2 DG A 2 N2 -0.106 REMARK 500 DA A 3 P DA A 3 OP1 -0.108 REMARK 500 DA A 3 C5' DA A 3 C4' 0.046 REMARK 500 DA A 3 C4' DA A 3 C3' 0.064 REMARK 500 DA A 3 O3' DA A 3 C3' -0.050 REMARK 500 DA A 3 C4 DA A 3 C5 -0.054 REMARK 500 DA A 3 C6 DA A 3 N1 -0.054 REMARK 500 DT A 4 P DT A 4 OP2 -0.128 REMARK 500 DT A 4 C4' DT A 4 C3' 0.103 REMARK 500 DT A 4 O4' DT A 4 C1' 0.070 REMARK 500 DC A 5 P DC A 5 O5' 0.075 REMARK 500 DC A 5 C5' DC A 5 C4' 0.058 REMARK 500 DC A 5 C2' DC A 5 C1' 0.065 REMARK 500 DC A 5 O4' DC A 5 C1' -0.075 REMARK 500 DC A 5 N1 DC A 5 C6 0.057 REMARK 500 DC A 5 C2 DC A 5 N3 -0.053 REMARK 500 DC A 5 N3 DC A 5 C4 0.082 REMARK 500 DG A 6 O4' DG A 6 C1' 0.076 REMARK 500 DG A 6 C6 DG A 6 N1 -0.068 REMARK 500 DG A 6 C8 DG A 6 N9 -0.057 REMARK 500 DG A 6 N9 DG A 6 C4 0.057 REMARK 500 DG A 6 C2 DG A 6 N2 -0.111 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC A 1 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = 6.5 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -8.3 DEGREES REMARK 500 DC A 1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = 11.9 DEGREES REMARK 500 DG A 2 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 2 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -9.4 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -8.9 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG A 2 C4 - C5 - C6 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 9.8 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = -8.4 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA A 3 O5' - C5' - C4' ANGL. DEV. = -14.4 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DT A 4 OP1 - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 DC A 5 OP1 - P - OP2 ANGL. DEV. = 9.5 DEGREES REMARK 500 DC A 5 O5' - P - OP1 ANGL. DEV. = -8.4 DEGREES REMARK 500 DC A 5 O5' - C5' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DC A 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 8.9 DEGREES REMARK 500 DC A 5 C6 - N1 - C2 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC A 5 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC A 5 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 5 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 6 O5' - P - OP1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG A 6 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 6 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 6 C5 - C6 - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DG A 6 N9 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 6 N3 - C2 - N2 ANGL. DEV. = -7.9 DEGREES REMARK 500 DG A 6 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM1 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 9 DBREF 1D10 A 1 6 PDB 1D10 1D10 1 6 SEQRES 1 A 6 DC DG DA DT DC DG HET DM1 A 7 38 HET SPM A 8 14 HET NA A 9 1 HETNAM DM1 DAUNOMYCIN HETNAM SPM SPERMINE HETNAM NA SODIUM ION HETSYN DM1 DAUNORUBICIN FORMUL 2 DM1 C27 H29 N O10 FORMUL 3 SPM C10 H26 N4 FORMUL 4 NA NA 1+ FORMUL 5 HOH *60(H2 O) SITE 1 AC1 9 DC A 1 DG A 2 DA A 3 DT A 4 SITE 2 AC1 9 DC A 5 DG A 6 SPM A 8 NA A 9 SITE 3 AC1 9 HOH A 32 SITE 1 AC2 10 DG A 2 DA A 3 DT A 4 DC A 5 SITE 2 AC2 10 DG A 6 DM1 A 7 HOH A 27 HOH A 50 SITE 3 AC2 10 HOH A 52 HOH A 59 SITE 1 AC3 5 DG A 6 DM1 A 7 HOH A 10 HOH A 11 SITE 2 AC3 5 HOH A 12 CRYST1 28.110 28.110 53.080 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 0.035575 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.035575 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.018839 0.00000 SCALE1 0.035575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.035575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018839 0.00000 ATOM 1 O5' DC A 1 9.520 20.252 22.862 1.00 17.54 O ATOM 2 C5' DC A 1 9.802 21.131 23.940 1.00 15.97 C ATOM 3 C4' DC A 1 11.222 21.217 24.215 1.00 15.67 C ATOM 4 O4' DC A 1 11.473 20.006 24.993 1.00 15.06 O ATOM 5 C3' DC A 1 12.223 21.079 22.993 1.00 15.99 C ATOM 6 O3' DC A 1 13.315 21.789 23.344 1.00 17.21 O ATOM 7 C2' DC A 1 12.409 19.530 22.903 1.00 15.07 C ATOM 8 C1' DC A 1 12.488 19.159 24.480 1.00 12.62 C ATOM 9 N1 DC A 1 12.025 17.728 24.613 1.00 10.58 N ATOM 10 C2 DC A 1 13.001 16.790 24.778 1.00 10.35 C ATOM 11 O2 DC A 1 14.201 17.090 24.866 1.00 10.86 O ATOM 12 N3 DC A 1 12.586 15.483 24.846 1.00 9.82 N ATOM 13 C4 DC A 1 11.261 15.032 24.843 1.00 9.44 C ATOM 14 N4 DC A 1 10.945 13.764 24.908 1.00 7.95 N ATOM 15 C5 DC A 1 10.298 16.078 24.628 1.00 10.40 C ATOM 16 C6 DC A 1 10.713 17.327 24.517 1.00 9.90 C ATOM 17 P DG A 2 13.868 22.938 22.322 1.00 19.49 P ATOM 18 OP1 DG A 2 14.887 23.642 23.123 1.00 20.48 O ATOM 19 OP2 DG A 2 12.717 23.398 21.674 1.00 19.42 O ATOM 20 O5' DG A 2 14.530 21.995 21.115 1.00 16.74 O ATOM 21 C5' DG A 2 15.791 21.446 21.457 1.00 14.84 C ATOM 22 C4' DG A 2 16.116 20.540 20.237 1.00 15.04 C ATOM 23 O4' DG A 2 15.218 19.504 20.173 1.00 14.05 O ATOM 24 C3' DG A 2 15.946 21.282 18.845 1.00 15.10 C ATOM 25 O3' DG A 2 17.057 20.812 18.142 1.00 18.91 O ATOM 26 C2' DG A 2 14.648 20.776 18.330 1.00 14.39 C ATOM 27 C1' DG A 2 14.825 19.219 18.798 1.00 12.04 C ATOM 28 N9 DG A 2 13.669 18.419 18.668 1.00 10.51 N ATOM 29 C8 DG A 2 12.360 18.786 18.634 1.00 9.59 C ATOM 30 N7 DG A 2 11.526 17.740 18.498 1.00 10.21 N ATOM 31 C5 DG A 2 12.351 16.683 18.375 1.00 9.02 C ATOM 32 C6 DG A 2 12.143 15.319 18.191 1.00 8.91 C ATOM 33 O6 DG A 2 10.992 14.785 18.133 1.00 10.35 O ATOM 34 N1 DG A 2 13.178 14.442 18.183 1.00 7.95 N ATOM 35 C2 DG A 2 14.425 14.979 18.321 1.00 7.10 C ATOM 36 N2 DG A 2 15.399 14.219 18.309 1.00 6.99 N ATOM 37 N3 DG A 2 14.786 16.206 18.481 1.00 8.24 N ATOM 38 C4 DG A 2 13.705 17.034 18.500 1.00 8.69 C ATOM 39 P DA A 3 18.010 21.803 17.222 1.00 21.51 P ATOM 40 OP1 DA A 3 18.615 22.654 18.120 1.00 20.89 O ATOM 41 OP2 DA A 3 17.052 22.157 16.116 1.00 22.11 O ATOM 42 O5' DA A 3 19.151 20.825 16.672 1.00 18.52 O ATOM 43 C5' DA A 3 20.074 20.316 17.655 1.00 16.75 C ATOM 44 C4' DA A 3 20.300 18.952 16.936 1.00 15.50 C ATOM 45 O4' DA A 3 19.068 18.194 17.017 1.00 13.53 O ATOM 46 C3' DA A 3 20.696 18.975 15.393 1.00 15.11 C ATOM 47 O3' DA A 3 21.868 18.275 15.285 1.00 15.15 O ATOM 48 C2' DA A 3 19.533 18.284 14.706 1.00 14.32 C ATOM 49 C1' DA A 3 18.920 17.372 15.823 1.00 12.43 C ATOM 50 N9 DA A 3 17.522 17.297 15.666 1.00 10.73 N ATOM 51 C8 DA A 3 16.662 18.326 15.622 1.00 10.55 C ATOM 52 N7 DA A 3 15.397 17.916 15.395 1.00 10.15 N ATOM 53 C5 DA A 3 15.520 16.535 15.318 1.00 10.00 C ATOM 54 C6 DA A 3 14.531 15.531 15.041 1.00 9.00 C ATOM 55 N6 DA A 3 13.218 15.768 14.922 1.00 8.94 N ATOM 56 N1 DA A 3 14.931 14.298 14.985 1.00 8.15 N ATOM 57 C2 DA A 3 16.284 14.070 15.158 1.00 9.23 C ATOM 58 N3 DA A 3 17.283 14.865 15.317 1.00 9.55 N ATOM 59 C4 DA A 3 16.786 16.137 15.394 1.00 9.75 C ATOM 60 P DT A 4 22.605 18.101 13.836 1.00 16.94 P ATOM 61 OP1 DT A 4 23.921 17.736 14.311 1.00 17.06 O ATOM 62 OP2 DT A 4 22.241 19.147 13.052 1.00 16.49 O ATOM 63 O5' DT A 4 21.995 16.674 13.295 1.00 16.36 O ATOM 64 C5' DT A 4 22.437 15.484 13.778 1.00 14.67 C ATOM 65 C4' DT A 4 21.692 14.386 13.059 1.00 13.05 C ATOM 66 O4' DT A 4 20.319 14.575 13.132 1.00 12.38 O ATOM 67 C3' DT A 4 22.098 14.454 11.480 1.00 14.49 C ATOM 68 O3' DT A 4 22.636 13.185 11.226 1.00 17.17 O ATOM 69 C2' DT A 4 20.790 14.654 10.753 1.00 12.58 C ATOM 70 C1' DT A 4 19.756 14.229 11.796 1.00 11.39 C ATOM 71 N1 DT A 4 18.463 14.949 11.752 1.00 10.89 N ATOM 72 C2 DT A 4 17.347 14.174 11.743 1.00 9.80 C ATOM 73 O2 DT A 4 17.392 12.938 11.678 1.00 11.32 O ATOM 74 N3 DT A 4 16.159 14.780 11.698 1.00 9.09 N ATOM 75 C4 DT A 4 15.997 16.140 11.725 1.00 9.65 C ATOM 76 O4 DT A 4 14.865 16.581 11.696 1.00 10.75 O ATOM 77 C5 DT A 4 17.188 16.962 11.783 1.00 10.34 C ATOM 78 C7 DT A 4 17.118 18.440 11.829 1.00 10.82 C ATOM 79 C6 DT A 4 18.377 16.321 11.825 1.00 10.50 C ATOM 80 P DC A 5 23.546 12.973 9.956 1.00 18.86 P ATOM 81 OP1 DC A 5 24.207 11.686 10.325 1.00 20.29 O ATOM 82 OP2 DC A 5 24.128 14.195 9.603 1.00 18.94 O ATOM 83 O5' DC A 5 22.571 12.371 8.744 1.00 16.83 O ATOM 84 C5' DC A 5 21.740 11.302 9.050 1.00 15.12 C ATOM 85 C4' DC A 5 20.665 11.394 7.909 1.00 14.76 C ATOM 86 O4' DC A 5 19.685 12.317 8.475 1.00 13.58 O ATOM 87 C3' DC A 5 21.002 11.933 6.491 1.00 14.40 C ATOM 88 O3' DC A 5 20.342 11.133 5.562 1.00 16.47 O ATOM 89 C2' DC A 5 20.410 13.337 6.432 1.00 12.68 C ATOM 90 C1' DC A 5 19.249 13.116 7.487 1.00 11.92 C ATOM 91 N1 DC A 5 18.551 14.335 7.875 1.00 10.24 N ATOM 92 C2 DC A 5 17.201 14.186 8.130 1.00 9.29 C ATOM 93 O2 DC A 5 16.738 13.035 8.162 1.00 9.73 O ATOM 94 N3 DC A 5 16.447 15.235 8.279 1.00 9.65 N ATOM 95 C4 DC A 5 16.928 16.568 8.300 1.00 9.86 C ATOM 96 N4 DC A 5 16.112 17.620 8.504 1.00 9.85 N ATOM 97 C5 DC A 5 18.356 16.747 8.112 1.00 9.70 C ATOM 98 C6 DC A 5 19.060 15.665 7.868 1.00 10.59 C ATOM 99 P DG A 6 21.145 10.034 4.702 1.00 19.22 P ATOM 100 OP1 DG A 6 21.651 9.053 5.656 1.00 18.49 O ATOM 101 OP2 DG A 6 22.043 10.904 3.854 1.00 18.06 O ATOM 102 O5' DG A 6 20.157 9.114 3.877 1.00 16.87 O ATOM 103 C5' DG A 6 19.198 8.392 4.576 1.00 15.55 C ATOM 104 C4' DG A 6 18.200 7.852 3.549 1.00 13.62 C ATOM 105 O4' DG A 6 17.355 8.977 3.159 1.00 13.42 O ATOM 106 C3' DG A 6 18.839 7.333 2.269 1.00 12.63 C ATOM 107 O3' DG A 6 18.060 6.246 1.896 1.00 13.69 O ATOM 108 C2' DG A 6 18.783 8.481 1.299 1.00 12.64 C ATOM 109 C1' DG A 6 17.456 9.219 1.686 1.00 11.57 C ATOM 110 N9 DG A 6 17.516 10.644 1.656 1.00 9.91 N ATOM 111 C8 DG A 6 18.550 11.458 1.710 1.00 9.54 C ATOM 112 N7 DG A 6 18.219 12.719 1.713 1.00 10.86 N ATOM 113 C5 DG A 6 16.837 12.698 1.636 1.00 9.99 C ATOM 114 C6 DG A 6 15.864 13.754 1.589 1.00 10.04 C ATOM 115 O6 DG A 6 16.174 14.986 1.628 1.00 11.67 O ATOM 116 N1 DG A 6 14.581 13.434 1.536 1.00 10.02 N ATOM 117 C2 DG A 6 14.242 12.120 1.517 1.00 9.53 C ATOM 118 N2 DG A 6 13.058 11.789 1.470 1.00 9.75 N ATOM 119 N3 DG A 6 15.056 11.062 1.554 1.00 8.79 N ATOM 120 C4 DG A 6 16.332 11.448 1.615 1.00 9.65 C TER 121 DG A 6 HETATM 122 C1 DM1 A 7 15.442 18.471 5.008 1.00 9.85 C HETATM 123 C2 DM1 A 7 16.644 19.206 5.019 1.00 9.83 C HETATM 124 C3 DM1 A 7 17.868 18.531 4.932 1.00 10.66 C HETATM 125 C4 DM1 A 7 17.902 17.139 4.863 1.00 9.90 C HETATM 126 O4 DM1 A 7 19.102 16.529 4.795 1.00 11.23 O HETATM 127 C5 DM1 A 7 16.680 16.370 4.922 1.00 9.66 C HETATM 128 C6 DM1 A 7 16.650 14.983 4.905 1.00 8.17 C HETATM 129 O6 DM1 A 7 17.753 14.276 4.801 1.00 10.35 O HETATM 130 C7 DM1 A 7 15.414 14.267 4.885 1.00 7.98 C HETATM 131 C8 DM1 A 7 15.410 12.865 4.858 1.00 8.32 C HETATM 132 O8 DM1 A 7 16.557 12.136 4.829 1.00 8.95 O HETATM 133 C9 DM1 A 7 14.140 12.158 4.871 1.00 8.24 C HETATM 134 C10 DM1 A 7 14.243 10.678 4.868 1.00 10.08 C HETATM 135 O10 DM1 A 7 14.922 10.432 6.141 1.00 13.17 O HETATM 136 C11 DM1 A 7 12.938 9.859 4.696 1.00 10.64 C HETATM 137 C12 DM1 A 7 11.778 10.648 5.447 1.00 11.23 C HETATM 138 O12 DM1 A 7 11.790 10.821 6.951 1.00 12.20 O HETATM 139 C13 DM1 A 7 10.479 9.896 5.212 1.00 12.91 C HETATM 140 O13 DM1 A 7 9.733 10.313 4.183 1.00 14.09 O HETATM 141 C14 DM1 A 7 10.164 8.718 6.072 1.00 14.04 C HETATM 142 C15 DM1 A 7 11.649 12.119 4.913 1.00 8.97 C HETATM 143 C16 DM1 A 7 12.922 12.871 4.896 1.00 7.54 C HETATM 144 C17 DM1 A 7 13.003 14.273 4.913 1.00 7.85 C HETATM 145 O17 DM1 A 7 11.780 14.925 4.872 1.00 9.51 O HETATM 146 C18 DM1 A 7 14.208 14.982 4.905 1.00 7.63 C HETATM 147 C19 DM1 A 7 14.243 16.403 4.942 1.00 8.21 C HETATM 148 O19 DM1 A 7 13.117 17.150 4.983 1.00 9.91 O HETATM 149 C20 DM1 A 7 15.469 17.062 4.970 1.00 8.84 C HETATM 150 C21 DM1 A 7 20.409 17.249 4.926 1.00 12.19 C HETATM 151 C1' DM1 A 7 15.791 9.288 6.458 1.00 14.52 C HETATM 152 C2' DM1 A 7 16.934 9.797 7.419 1.00 15.26 C HETATM 153 C3' DM1 A 7 16.334 10.054 8.864 1.00 15.60 C HETATM 154 N3' DM1 A 7 17.456 10.460 9.771 1.00 13.77 N HETATM 155 C4' DM1 A 7 15.543 8.761 9.352 1.00 15.76 C HETATM 156 O4' DM1 A 7 16.567 7.719 9.356 1.00 18.22 O HETATM 157 C5' DM1 A 7 14.461 8.366 8.376 1.00 15.13 C HETATM 158 O5' DM1 A 7 14.971 8.210 7.027 1.00 15.54 O HETATM 159 C6' DM1 A 7 13.677 7.086 8.710 1.00 15.89 C HETATM 160 N1 SPM A 8 9.289 18.841 8.877 1.00 42.53 N HETATM 161 C2 SPM A 8 10.079 18.950 10.240 1.00 42.31 C HETATM 162 C3 SPM A 8 10.525 17.672 10.982 1.00 41.36 C HETATM 163 C4 SPM A 8 9.581 16.893 11.818 1.00 40.34 C HETATM 164 N5 SPM A 8 8.973 15.536 11.427 1.00 39.06 N HETATM 165 C6 SPM A 8 8.666 14.627 12.544 1.00 38.30 C HETATM 166 C7 SPM A 8 9.388 14.794 13.846 1.00 38.00 C HETATM 167 C8 SPM A 8 8.870 14.567 15.141 1.00 38.38 C HETATM 168 C9 SPM A 8 7.394 14.321 15.531 1.00 39.01 C HETATM 169 N10 SPM A 8 7.013 12.817 15.775 1.00 39.54 N HETATM 170 C11 SPM A 8 7.044 12.404 17.330 1.00 39.98 C HETATM 171 C12 SPM A 8 7.847 11.151 17.624 1.00 39.40 C HETATM 172 C13 SPM A 8 7.752 9.974 18.384 1.00 39.33 C HETATM 173 N14 SPM A 8 8.480 8.688 17.870 1.00 39.87 N HETATM 174 NA NA A 9 13.247 8.320 24.155 1.00 32.32 NA HETATM 175 O HOH A 10 22.086 13.800 3.151 1.00 41.33 O HETATM 176 O HOH A 11 18.055 16.752 1.357 1.00 34.97 O HETATM 177 O HOH A 12 21.319 16.285 0.748 1.00 42.24 O HETATM 178 O HOH A 13 14.119 20.158 1.552 1.00 37.07 O HETATM 179 O HOH A 14 14.898 22.259 2.857 1.00 44.16 O HETATM 180 O HOH A 15 17.513 22.882 4.126 1.00 41.15 O HETATM 181 O HOH A 16 19.755 21.795 5.234 1.00 41.63 O HETATM 182 O HOH A 17 20.210 6.590 7.619 1.00 42.79 O HETATM 183 O HOH A 18 17.673 5.925 6.955 1.00 43.00 O HETATM 184 O HOH A 19 15.317 5.734 4.661 1.00 44.64 O HETATM 185 O HOH A 20 14.309 8.744 1.362 1.00 28.66 O HETATM 186 O HOH A 21 7.361 18.508 23.846 1.00 29.70 O HETATM 187 O HOH A 22 11.693 9.549 1.238 1.00 39.13 O HETATM 188 O HOH A 23 30.455 11.948 11.842 1.00 53.35 O HETATM 189 O HOH A 24 26.912 15.352 5.365 1.00 51.86 O HETATM 190 O HOH A 25 11.315 24.672 5.532 1.00 48.60 O HETATM 191 O HOH A 26 10.461 25.334 22.825 1.00 29.19 O HETATM 192 O HOH A 27 20.694 18.432 10.675 1.00 24.74 O HETATM 193 O HOH A 28 15.987 0.291 1.378 1.00 44.39 O HETATM 194 O HOH A 29 16.192 2.783 -0.170 1.00 40.79 O HETATM 195 O HOH A 30 15.337 5.582 1.220 1.00 43.69 O HETATM 196 O HOH A 31 8.100 15.545 18.698 1.00 38.57 O HETATM 197 O HOH A 32 7.539 8.812 3.454 1.00 43.46 O HETATM 198 O HOH A 33 11.123 5.619 5.527 1.00 46.33 O HETATM 199 O HOH A 34 8.931 21.388 19.878 1.00 35.49 O HETATM 200 O HOH A 35 19.970 22.961 20.190 1.00 32.38 O HETATM 201 O HOH A 36 23.646 10.492 12.974 1.00 37.81 O HETATM 202 O HOH A 37 13.631 23.987 15.981 1.00 47.20 O HETATM 203 O HOH A 38 13.064 26.920 5.053 1.00 49.01 O HETATM 204 O HOH A 39 16.616 9.510 12.718 1.00 19.36 O HETATM 205 O HOH A 40 26.676 16.372 1.068 1.00 51.44 O HETATM 206 O HOH A 41 9.268 12.038 1.582 1.00 30.67 O HETATM 207 O HOH A 42 11.350 22.086 18.894 1.00 31.82 O HETATM 208 O HOH A 43 22.524 15.684 7.646 1.00 28.72 O HETATM 209 O HOH A 44 9.503 1.274 24.276 1.00 46.08 O HETATM 210 O HOH A 45 23.559 15.311 4.692 1.00 47.99 O HETATM 211 O HOH A 46 24.807 10.239 2.269 1.00 49.20 O HETATM 212 O HOH A 47 8.220 17.077 20.869 1.00 47.80 O HETATM 213 O HOH A 48 0.824 7.964 13.121 1.00 49.79 O HETATM 214 O HOH A 49 12.302 24.190 8.633 1.00 52.72 O HETATM 215 O HOH A 50 22.157 18.198 8.486 1.00 46.13 O HETATM 216 O HOH A 51 19.578 8.171 10.121 1.00 25.61 O HETATM 217 O HOH A 52 6.804 13.246 13.229 1.00 39.26 O HETATM 218 O HOH A 53 11.250 8.544 28.355 1.00 43.77 O HETATM 219 O HOH A 54 24.251 14.923 1.056 1.00 44.31 O HETATM 220 O HOH A 55 17.487 6.628 12.919 1.00 41.91 O HETATM 221 O HOH A 56 20.621 5.959 25.581 1.00 42.04 O HETATM 222 O HOH A 57 17.780 5.894 25.736 1.00 43.05 O HETATM 223 O HOH A 58 18.531 3.536 20.349 1.00 42.18 O HETATM 224 O HOH A 59 6.103 16.840 15.455 1.00 39.13 O HETATM 225 O HOH A 60 31.087 16.418 9.341 1.00 47.26 O HETATM 226 O HOH A 61 9.355 6.382 3.310 1.00 57.53 O HETATM 227 O HOH A 62 22.792 17.825 2.236 1.00 40.25 O HETATM 228 O HOH A 63 1.620 15.649 14.321 1.00 50.67 O HETATM 229 O HOH A 64 21.075 19.405 1.464 1.00 46.90 O HETATM 230 O HOH A 65 3.164 13.991 19.689 1.00 63.01 O HETATM 231 O HOH A 66 6.186 10.017 12.817 1.00 56.00 O HETATM 232 O HOH A 67 16.213 22.438 25.523 1.00 61.92 O HETATM 233 O HOH A 68 9.108 24.140 20.730 1.00 30.50 O HETATM 234 O HOH A 69 24.802 13.350 2.949 1.00 47.08 O CONECT 122 123 149 CONECT 123 122 124 CONECT 124 123 125 CONECT 125 124 126 127 CONECT 126 125 150 CONECT 127 125 128 149 CONECT 128 127 129 130 CONECT 129 128 CONECT 130 128 131 146 CONECT 131 130 132 133 CONECT 132 131 CONECT 133 131 134 143 CONECT 134 133 135 136 CONECT 135 134 151 CONECT 136 134 137 CONECT 137 136 138 139 142 CONECT 138 137 CONECT 139 137 140 141 CONECT 140 139 CONECT 141 139 CONECT 142 137 143 CONECT 143 133 142 144 CONECT 144 143 145 146 CONECT 145 144 CONECT 146 130 144 147 CONECT 147 146 148 149 CONECT 148 147 CONECT 149 122 127 147 CONECT 150 126 CONECT 151 135 152 158 CONECT 152 151 153 CONECT 153 152 154 155 CONECT 154 153 CONECT 155 153 156 157 CONECT 156 155 CONECT 157 155 158 159 CONECT 158 151 157 CONECT 159 157 CONECT 160 161 CONECT 161 160 162 CONECT 162 161 163 CONECT 163 162 164 CONECT 164 163 165 CONECT 165 164 166 CONECT 166 165 167 CONECT 167 166 168 CONECT 168 167 169 CONECT 169 168 170 CONECT 170 169 171 CONECT 171 170 172 CONECT 172 171 173 CONECT 173 172 MASTER 324 0 3 0 0 0 8 6 233 1 52 1 END