PDB Short entry for 1KSB HEADER DNA 11-JAN-02 1KSB TITLE RELATIONSHIP OF SOLUTION AND PROTEIN-BOUND STRUCTURES OF DNA DUPLEXES TITLE 2 WITH THE MAJOR INTRASTRAND CROSS-LINK LESIONS FORMED ON CISPLATIN TITLE 3 BINDING TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*TP*CP*CP*GP*GP*CP*CP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CISPLATIN INTRASTRAND CROSS-LINK DNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*AP*GP*GP*CP*CP*GP*GP*AP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, CISPLATIN, DNA, DUPLEX, 9-MER, INTRASTRAND KEYWDS 2 CROSS-LINK, MODEL J EXPDTA SOLUTION NMR AUTHOR L.G.MARZILLI,J.S.SAAD,Z.KUKLENYIK,K.A.KEATING,Y.XU REVDAT 5 01-MAY-24 1KSB 1 REMARK LINK REVDAT 4 13-JUL-11 1KSB 1 VERSN REVDAT 3 23-JUN-10 1KSB 1 HET REVDAT 2 24-FEB-09 1KSB 1 VERSN REVDAT 1 17-JAN-02 1KSB 0 JRNL AUTH L.G.MARZILLI,J.S.SAAD,Z.KUKLENYIK,K.A.KEATING,Y.XU JRNL TITL RELATIONSHIP OF SOLUTION AND PROTEIN-BOUND STRUCTURES OF DNA JRNL TITL 2 DUPLEXES WITH THE MAJOR INTRASTRAND CROSS-LINK LESIONS JRNL TITL 3 FORMED ON CISPLATIN BINDING TO DNA. JRNL REF J.AM.CHEM.SOC. V. 123 2764 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11456962 JRNL DOI 10.1021/JA0007915 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.0, DISCOVER, IRMA REMARK 3 AUTHORS : BIOSYM/MSI (DISCOVER), BIOSYM/MSI (IRMA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOE-RESTRAINED REFINEMENT REMARK 3 (DETAILS CAN BE FOUND IN THE PAPER) REMARK 4 REMARK 4 1KSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015290. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : PLATINATED 9-MER DUPLEX REMARK 210 DISSOLVED IN D2O/H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : OMEGA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : GE; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : INSIGHT II, CURVES REMARK 210 METHOD USED : AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 2D 1H-31P PHASE-SENSITIVE REVERSE CHEMICAL SHIFT REMARK 210 CORRELATION (RCSC) AND 1H-13C MAGNITUDE MODE HMQC EXPERIMENTS REMARK 210 WERE PERFORMED. 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 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: 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 B 4 C5' DC B 4 C4' 0.046 REMARK 500 DC B 4 O3' DC B 4 C3' -0.110 REMARK 500 DC B 5 O3' DC B 5 C3' -0.050 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 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 5 O4' - C1' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG B 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 2 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 DG B 3 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 DG B 3 C3' - C2' - C1' ANGL. DEV. = 9.5 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 DG B 3 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC B 5 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 8 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES 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 DC A 1 0.07 SIDE CHAIN REMARK 500 DG B 2 0.11 SIDE CHAIN REMARK 500 DG B 3 0.11 SIDE CHAIN REMARK 500 DC B 4 0.09 SIDE CHAIN REMARK 500 DG B 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 10 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 N7 REMARK 620 2 CPT A 10 N1 178.5 REMARK 620 3 CPT A 10 N2 90.4 90.4 REMARK 620 4 DG A 6 N7 88.6 90.5 178.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT A 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CKT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED REMARK 900 DNA DUPLEX REMARK 900 RELATED ID: 1A84 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS- REMARK 900 DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK, THE MAJOR REMARK 900 ADDUCT OF THE ANTICANCER DRUG CISPLATIN DBREF 1KSB A 1 9 PDB 1KSB 1KSB 1 9 DBREF 1KSB B 1 9 PDB 1KSB 1KSB 1 9 SEQRES 1 A 9 DC DT DC DC DG DG DC DC DT SEQRES 1 B 9 DA DG DG DC DC DG DG DA DG HET CPT A 10 9 HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 3 CPT CL2 H6 N2 PT LINK N7 DG A 5 PT1 CPT A 10 1555 1555 2.01 LINK N7 DG A 6 PT1 CPT A 10 1555 1555 2.01 SITE 1 AC1 2 DG A 5 DG A 6 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