Header list of 1ksb.pdb file
Complete list - 25 201 Bytes
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 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 : DISCOVER, IRMA
REMARK 3 AUTHORS : BIOSYM/MSI (DISCOVER), BIOSYM/MSI (IRMA)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 NOE-RESTRAINED REFINEMENT
REMARK 3 (DETAILS CAN BE FOUND IN THE PAPER)
REMARK 4
REMARK 4 1KSB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-02.
REMARK 100 THE RCSB ID CODE IS RCSB015290.
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 : FELIX 97.0, 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. = 3.9 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-
REMARK 900 MODIFIED DNA DUPLEX
REMARK 900 RELATED ID: 1A84 RELATED DB: PDB
REMARK 900 NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING
REMARK 900 A CIS-DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK,
REMARK 900 THE MAJOR 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 PT1 CPT A 10 N7 DG A 5 1555 1555 2.01
LINK PT1 CPT A 10 N7 DG A 6 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
Complete list - 25 201 Bytes