Header list of 1a84.pdb file
Complete list - 25 201 Bytes
HEADER DNA 02-APR-98 1A84
TITLE NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING A CIS-
TITLE 2 DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK, THE MAJOR ADDUCT
TITLE 3 OF THE ANTICANCER DRUG CISPLATIN, 1 STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA D(CCTCTG*G*TCTCC);
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: CISPLATIN INTRASTRAND CROSS-LINKED DNA;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA D(GGAGACCAGAGG);
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: CISPLATIN INTRASTRAND CROSS-LINKED DNA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DEOXYRIBONUCLEIC ACID, CISPLATIN, DNA, DUPLEX, DODECAMER, HMG-DOMAIN
KEYWDS 2 INTERACTION
EXPDTA SOLUTION NMR
AUTHOR A.GELASCO,S.J.LIPPARD
REVDAT 4 13-JUL-11 1A84 1 VERSN
REVDAT 3 23-JUN-10 1A84 1 FORMUL
REVDAT 2 24-FEB-09 1A84 1 VERSN
REVDAT 1 25-NOV-98 1A84 0
JRNL AUTH A.GELASCO,S.J.LIPPARD
JRNL TITL NMR SOLUTION STRUCTURE OF A DNA DODECAMER DUPLEX CONTAINING
JRNL TITL 2 A CIS-DIAMMINEPLATINUM(II) D(GPG) INTRASTRAND CROSS-LINK,
JRNL TITL 3 THE MAJOR ADDUCT OF THE ANTICANCER DRUG CISPLATIN.
JRNL REF BIOCHEMISTRY V. 37 9230 1998
JRNL REFN ISSN 0006-2960
JRNL PMID 9649303
JRNL DOI 10.1021/BI973176V
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1A84 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288
REMARK 210 PH : 6.9
REMARK 210 IONIC STRENGTH : 100 MM NACL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : D2O/H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D1HNOESY; TOCSY; PECOSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ
REMARK 210 SPECTROMETER MODEL : FBML 750
REMARK 210 SPECTROMETER MANUFACTURER : FRANCIS BITTER MAGNET LAB CUSTOM
REMARK 210 BUILT
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR, QUANTA
REMARK 210 METHOD USED : NOE-RESTRAINED REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D 1H-1H NMR
REMARK 210 SPECTROSCOPY IN BOTH D2O AND H2O SOLUTIONS
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: 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 H4' DA B 15 OP1 DG B 16 1.48
REMARK 500 H2'' DG B 23 OP2 DG B 24 1.57
REMARK 500 H2'' DT A 10 OP2 DC A 11 1.60
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 DT A 8 C5' DT A 8 C4' 0.048
REMARK 500 DT A 10 C5 DT A 10 C7 0.038
REMARK 500 DC A 12 C5' DC A 12 C4' 0.059
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 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES
REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DT A 5 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES
REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DC A 11 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES
REMARK 500 DC A 11 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DC A 12 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES
REMARK 500 DC A 12 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES
REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG B 13 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES
REMARK 500 DG B 13 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG B 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DG B 14 C4' - C3' - C2' ANGL. DEV. = 5.4 DEGREES
REMARK 500 DG B 14 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG B 14 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DA B 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DA B 15 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DG B 16 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DA B 17 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES
REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA B 17 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC B 18 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES
REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DC B 19 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES
REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DA B 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DA B 20 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DG B 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG B 21 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DA B 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DA B 22 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DG B 23 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 23 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DG B 23 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES
REMARK 500 DG B 24 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 52 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 DC A 9 0.08 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 13 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG A 6 N7
REMARK 620 2 CPT A 13 N1 179.9
REMARK 620 3 CPT A 13 N2 89.8 90.1
REMARK 620 4 DG A 7 N7 90.1 90.0 179.7
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 13
DBREF 1A84 A 1 12 PDB 1A84 1A84 1 12
DBREF 1A84 B 13 24 PDB 1A84 1A84 13 24
SEQRES 1 A 12 DC DC DT DC DT DG DG DT DC DT DC DC
SEQRES 1 B 12 DG DG DA DG DA DC DC DA DG DA DG DG
HET CPT A 13 9
HETNAM CPT CISPLATIN
HETSYN CPT DIAMMINE(DICHLORO)PLATINUM
FORMUL 3 CPT CL2 H6 N2 PT
LINK PT1 CPT A 13 N7 DG A 6 1555 1555 2.05
LINK PT1 CPT A 13 N7 DG A 7 1555 1555 2.05
SITE 1 AC1 3 DT A 5 DG A 6 DG A 7
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