PDB Short entry for 1PIK HEADER DNA 11-DEC-96 1PIK TITLE ESPERAMICIN A1-DNA COMPLEX, NMR, 4 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEXED WITH ESPERAMICIN A1 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DRUG COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR R.A.KUMAR,N.IKEMOTO,D.J.PATEL REVDAT 3 29-JUL-20 1PIK 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1PIK 1 VERSN REVDAT 1 12-MAR-97 1PIK 0 JRNL AUTH R.A.KUMAR,N.IKEMOTO,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE ESPERAMICIN A1-DNA COMPLEX JRNL REF J.MOL.BIOL. V. 265 173 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9020981 JRNL DOI 10.1006/JMBI.1996.0719 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.IKEMOTO,R.A.KUMAR,P.C.DEDON,S.J.DANISHEFSKY,D.J.PATEL REMARK 1 TITL ESPERAMICIN A1 INTERCALATES INTO DUPLEX DNA FROM THE MINOR REMARK 1 TITL 2 GROOVE REMARK 1 REF J.AM.CHEM.SOC. V. 116 9387 1994 REMARK 1 REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PIK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175698. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, XEASY, RPEAK, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 4 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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, B, C 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1 DPA A 25 O3 DLF B 24 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 1 DC A 1 C5' DC A 1 C4' 0.052 REMARK 500 1 DG A 2 C5' DG A 2 C4' 0.046 REMARK 500 1 DA A 4 N9 DA A 4 C4 0.044 REMARK 500 1 DC A 6 C5' DC A 6 C4' 0.045 REMARK 500 1 DC A 7 C5' DC A 7 C4' 0.055 REMARK 500 1 DG A 8 C5' DG A 8 C4' 0.049 REMARK 500 1 DC B 11 C5' DC B 11 C4' 0.045 REMARK 500 1 DG B 13 C5' DG B 13 C4' 0.063 REMARK 500 1 DA B 14 N9 DA B 14 C4 0.039 REMARK 500 1 DC B 16 C5' DC B 16 C4' 0.053 REMARK 500 1 DC B 16 C2' DC B 16 C1' 0.061 REMARK 500 1 DC B 17 C5' DC B 17 C4' 0.043 REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.045 REMARK 500 2 DG A 3 C5' DG A 3 C4' 0.046 REMARK 500 2 DA A 4 N9 DA A 4 C4 0.051 REMARK 500 2 DT A 5 N1 DT A 5 C2 0.051 REMARK 500 2 DC A 7 C5' DC A 7 C4' 0.062 REMARK 500 2 DC A 7 C3' DC A 7 C2' 0.074 REMARK 500 2 DG B 13 C5' DG B 13 C4' 0.068 REMARK 500 2 DT B 15 C3' DT B 15 C2' 0.085 REMARK 500 2 DC B 16 C5' DC B 16 C4' 0.047 REMARK 500 2 DC B 17 C5' DC B 17 C4' 0.052 REMARK 500 2 DG B 18 C5' DG B 18 C4' 0.050 REMARK 500 3 DG A 2 C5' DG A 2 C4' 0.043 REMARK 500 3 DG A 3 C3' DG A 3 C2' 0.082 REMARK 500 3 DG A 3 N9 DG A 3 C4 0.050 REMARK 500 3 DC A 7 C5' DC A 7 C4' 0.062 REMARK 500 3 DG B 12 C5' DG B 12 C4' 0.045 REMARK 500 3 DG B 13 C5' DG B 13 C4' 0.049 REMARK 500 3 DA B 14 N9 DA B 14 C4 0.039 REMARK 500 3 DC B 16 C5' DC B 16 C4' 0.050 REMARK 500 3 DG B 18 C5' DG B 18 C4' 0.042 REMARK 500 4 DG A 2 N9 DG A 2 C4 0.052 REMARK 500 4 DT A 5 N1 DT A 5 C2 0.056 REMARK 500 4 DC A 7 N1 DC A 7 C6 0.037 REMARK 500 4 DA B 14 N9 DA B 14 C4 0.042 REMARK 500 4 DC B 16 N1 DC B 16 C6 0.037 REMARK 500 4 DG B 18 C5' DG B 18 C4' 0.047 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 1 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DG A 3 P - O5' - C5' ANGL. DEV. = 12.1 DEGREES REMARK 500 1 DG A 3 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = 14.7 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 22.0 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES REMARK 500 1 DC A 6 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC A 6 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC A 7 C3' - O3' - P ANGL. DEV. = 20.4 DEGREES REMARK 500 1 DG A 8 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES REMARK 500 1 DG A 8 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DC B 11 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DG B 12 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES REMARK 500 1 DG B 12 C3' - O3' - P ANGL. DEV. = 20.7 DEGREES REMARK 500 1 DG B 13 P - O5' - C5' ANGL. DEV. = 15.4 DEGREES REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 12.8 DEGREES REMARK 500 1 DA B 14 P - O5' - C5' ANGL. DEV. = 18.5 DEGREES REMARK 500 1 DA B 14 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES REMARK 500 1 DT B 15 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 15 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DC B 16 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC B 16 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DC B 17 P - O5' - C5' ANGL. DEV. = 16.3 DEGREES REMARK 500 1 DC B 17 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC B 17 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DC B 17 C3' - O3' - P ANGL. DEV. = 14.9 DEGREES REMARK 500 1 DG B 18 P - O5' - C5' ANGL. DEV. = 15.9 DEGREES REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DC A 1 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 2 DG A 3 P - O5' - C5' ANGL. DEV. = 10.3 DEGREES REMARK 500 2 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DG A 3 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 3 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 162 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DC A 1 0.12 SIDE CHAIN REMARK 500 1 DG A 3 0.08 SIDE CHAIN REMARK 500 1 DT A 5 0.07 SIDE CHAIN REMARK 500 1 DG A 8 0.08 SIDE CHAIN REMARK 500 1 DC B 11 0.09 SIDE CHAIN REMARK 500 1 DA B 14 0.06 SIDE CHAIN REMARK 500 2 DC A 1 0.07 SIDE CHAIN REMARK 500 2 DG A 3 0.08 SIDE CHAIN REMARK 500 2 DC A 6 0.09 SIDE CHAIN REMARK 500 2 DC A 7 0.12 SIDE CHAIN REMARK 500 2 DC B 11 0.12 SIDE CHAIN REMARK 500 2 DA B 14 0.12 SIDE CHAIN REMARK 500 3 DC A 1 0.14 SIDE CHAIN REMARK 500 3 DA A 4 0.07 SIDE CHAIN REMARK 500 3 DT A 5 0.13 SIDE CHAIN REMARK 500 3 DC A 6 0.08 SIDE CHAIN REMARK 500 3 DC A 7 0.13 SIDE CHAIN REMARK 500 3 DC B 11 0.08 SIDE CHAIN REMARK 500 3 DG B 12 0.06 SIDE CHAIN REMARK 500 3 DA B 14 0.10 SIDE CHAIN REMARK 500 4 DA A 4 0.06 SIDE CHAIN REMARK 500 4 DC A 6 0.08 SIDE CHAIN REMARK 500 4 DG A 8 0.06 SIDE CHAIN REMARK 500 4 DC B 11 0.09 SIDE CHAIN REMARK 500 4 DA B 14 0.09 SIDE CHAIN REMARK 500 4 DC B 16 0.08 SIDE CHAIN REMARK 500 4 DC B 17 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1PIK A 1 8 PDB 1PIK 1PIK 1 8 DBREF 1PIK B 11 18 PDB 1PIK 1PIK 11 18 SEQRES 1 A 8 DC DG DG DA DT DC DC DG SEQRES 1 B 8 DC DG DG DA DT DC DC DG HET DAG C 1 21 HET MAT C 2 31 HET DPA A 25 33 HET TMR B 22 24 HET DLF B 24 20 HET MTC B 26 41 HETNAM DAG 4-AMINO-4,6-DIDEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAT 2,4-DIDEOXY-3-O-METHYL-4-(PROPAN-2-YLAMINO)-ALPHA-L- HETNAM 2 MAT THREO-PENTOPYRANOSE HETNAM DPA 4,5-DIMETHOXY-N-(2'-METHOXYPROPENOYL ANTHRANILATE) HETNAM TMR 2,6-DIDEOXY-4-S-METHYL-4-THIO-BETA-D-RIBO-HEXOPYRANOSE HETNAM DLF 2-DEOXY-ALPHA-L-FUCOPYRANOSE HETNAM MTC [1,8-DIHYDROXY-11-OXO-13-(2-METHYLTRITHIO-ETHYLIDENE)- HETNAM 2 MTC BICYCLO[7.3.1]TRIDECA-4,9-DIENE-2,6-DIYN-10-YL]- HETNAM 3 MTC CARBAMIC ACID METHYL ESTER FORMUL 3 DAG C6 H13 N O4 FORMUL 3 MAT C9 H19 N O3 FORMUL 4 DPA C13 H15 N O5 FORMUL 5 TMR C7 H14 O3 S FORMUL 6 DLF C6 H12 O4 FORMUL 7 MTC C18 H17 N O4 S3 LINK C1 DPA A 25 O3 DLF B 24 1555 1555 1.31 LINK O1 TMR B 22 N4 DAG C 1 1555 1555 1.46 LINK O1 DLF B 24 C9 MTC B 26 1555 1555 1.44 LINK C1 MTC B 26 O1 DAG C 1 1555 1555 1.43 LINK O2 DAG C 1 C1 MAT C 2 1555 1555 1.40 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000