HEADER DNA 26-OCT-95 1DDP TITLE SOLUTION STRUCTURE OF A CISPLATIN-INDUCED [CATAGCTATG]2 INTERSTRAND TITLE 2 CROSS-LINK COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*TP*AP*GP*CP*TP*AP*TP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, DOUBLE HELIX, ANTITUMOR DRUG, CIS-DDP, INTERSTRAND CROSS-LINK EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR L.ZHU,H.HUANG,B.R.REID,G.P.DROBNY,P.B.HOPKINS REVDAT 5 13-MAR-24 1DDP 1 COMPND SOURCE REMARK REVDAT 4 13-JUL-11 1DDP 1 VERSN REVDAT 3 23-JUN-10 1DDP 1 HET REVDAT 2 24-FEB-09 1DDP 1 VERSN REVDAT 1 08-MAR-96 1DDP 0 JRNL AUTH H.HUANG,L.ZHU,B.R.REID,G.P.DROBNY,P.B.HOPKINS JRNL TITL SOLUTION STRUCTURE OF A CISPLATIN-INDUCED DNA INTERSTRAND JRNL TITL 2 CROSS-LINK. JRNL REF SCIENCE V. 270 1842 1995 JRNL REFN ISSN 0036-8075 JRNL PMID 8525382 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : BIOSYM TECHNOLOGIES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL RMS COORD. SHIFT 0.55 ANGSTROMS REMARK 3 NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 643 NUMBER OF HETEROGEN ATOMS 0 REMARK 3 NUMBER OF SOLVENT ATOMS 0 AMBER FORCE FIELDS USED REMARK 4 REMARK 4 1DDP 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_1000172746. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL 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 : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: BECAUSE THE BOND LENGTH BETWEEN PT AND N7 IN THE CISPLATIN REMARK 210 CROSS-LINK IS LONGER THAN 2.00 ANGSTROMS, THE PT-N7 BONDS MIGHT REMARK 210 NOT APPEAR WHEN A PROGRAM READS THIS ENTRY. 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 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 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA B 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC B 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA B 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA B 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC B 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 9 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA B 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC B 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DA B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT B 9 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DA A 4 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 158 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 DA A 2 0.05 SIDE CHAIN REMARK 500 1 DT A 3 0.06 SIDE CHAIN REMARK 500 1 DG A 5 0.07 SIDE CHAIN REMARK 500 1 DA A 8 0.05 SIDE CHAIN REMARK 500 1 DA B 2 0.05 SIDE CHAIN REMARK 500 1 DT B 3 0.06 SIDE CHAIN REMARK 500 1 DG B 5 0.07 SIDE CHAIN REMARK 500 1 DA B 8 0.06 SIDE CHAIN REMARK 500 2 DA A 2 0.06 SIDE CHAIN REMARK 500 2 DT A 3 0.07 SIDE CHAIN REMARK 500 2 DG A 5 0.07 SIDE CHAIN REMARK 500 2 DA A 8 0.06 SIDE CHAIN REMARK 500 2 DA B 2 0.05 SIDE CHAIN REMARK 500 2 DT B 3 0.07 SIDE CHAIN REMARK 500 2 DG B 5 0.07 SIDE CHAIN REMARK 500 2 DA B 8 0.06 SIDE CHAIN REMARK 500 3 DA A 2 0.05 SIDE CHAIN REMARK 500 3 DT A 3 0.06 SIDE CHAIN REMARK 500 3 DG A 5 0.07 SIDE CHAIN REMARK 500 3 DA A 8 0.05 SIDE CHAIN REMARK 500 3 DA B 2 0.05 SIDE CHAIN REMARK 500 3 DT B 3 0.06 SIDE CHAIN REMARK 500 3 DG B 5 0.07 SIDE CHAIN REMARK 500 3 DA B 8 0.06 SIDE CHAIN REMARK 500 4 DT A 3 0.06 SIDE CHAIN REMARK 500 4 DG A 5 0.07 SIDE CHAIN REMARK 500 4 DA A 8 0.05 SIDE CHAIN REMARK 500 4 DA B 2 0.06 SIDE CHAIN REMARK 500 4 DG B 5 0.07 SIDE CHAIN REMARK 500 4 DA B 8 0.06 SIDE CHAIN REMARK 500 5 DG A 5 0.07 SIDE CHAIN REMARK 500 5 DG A 10 0.06 SIDE CHAIN REMARK 500 5 DA B 2 0.06 SIDE CHAIN REMARK 500 5 DT B 3 0.06 SIDE CHAIN REMARK 500 5 DG B 5 0.07 SIDE CHAIN REMARK 500 6 DT A 3 0.06 SIDE CHAIN REMARK 500 6 DG A 5 0.07 SIDE CHAIN REMARK 500 6 DA A 8 0.06 SIDE CHAIN REMARK 500 6 DG A 10 0.06 SIDE CHAIN REMARK 500 6 DA B 2 0.09 SIDE CHAIN REMARK 500 6 DG B 5 0.07 SIDE CHAIN REMARK 500 6 DA B 8 0.06 SIDE CHAIN REMARK 500 7 DA A 2 0.06 SIDE CHAIN REMARK 500 7 DT A 3 0.06 SIDE CHAIN REMARK 500 7 DG A 5 0.07 SIDE CHAIN REMARK 500 7 DG A 10 0.06 SIDE CHAIN REMARK 500 7 DT B 3 0.06 SIDE CHAIN REMARK 500 7 DG B 5 0.07 SIDE CHAIN REMARK 500 7 DA B 8 0.06 SIDE CHAIN REMARK 500 8 DA A 2 0.05 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 72 PLANE DEVIATIONS. 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 11 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 N7 REMARK 620 2 CPT A 11 N1 89.0 REMARK 620 3 CPT A 11 N2 178.8 89.9 REMARK 620 4 DG B 5 N7 92.2 178.8 89.0 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 11 DBREF 1DDP A 1 10 PDB 1DDP 1DDP 1 10 DBREF 1DDP B 1 10 PDB 1DDP 1DDP 1 10 SEQRES 1 A 10 DC DA DT DA DG DC DT DA DT DG SEQRES 1 B 10 DC DA DT DA DG DC DT DA DT DG HET CPT A 11 9 HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 3 CPT CL2 H6 N2 PT LINK N7 DG A 5 PT1 CPT A 11 1555 1555 2.01 LINK PT1 CPT A 11 N7 DG B 5 1555 1555 2.01 SITE 1 AC1 2 DG A 5 DG B 5 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 MODEL 1