Header list of 1au6.pdb file
Complete list - 16 202 Bytes
HEADER DNA 11-SEP-97 1AU6
TITLE SOLUTION STRUCTURE OF DNA D(CATGCATG) INTERSTRAND-CROSSLINKED BY
TITLE 2 BISPLATIN COMPOUND (1,1/T,T), NMR, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: BISPLATINUM COMPOUND (1,1/T,T) INTERSTRAND-CROSSLINKED
COMPND 6 DNA OCTAMER
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS BISPLATINUM COMPOUND (1, 1/T, T), DNA, INTERSTRAND CROSSLINK,
KEYWDS 2 DUMBBELL STRUCTURE, DEOXYRIBONUCLEIC ACID
EXPDTA SOLUTION NMR
AUTHOR D.YANG,S.S.G.E.VAN BOOM,J.REEDIJK,J.H.VAN BOOM,N.FARRELL,A.H.-J.WANG
REVDAT 4 16-FEB-22 1AU6 1 REMARK LINK
REVDAT 3 24-FEB-09 1AU6 1 VERSN
REVDAT 2 01-APR-03 1AU6 1 JRNL
REVDAT 1 25-FEB-98 1AU6 0
JRNL AUTH D.YANG,S.S.VAN BOOM,J.REEDIJK,J.H.VAN BOOM,N.FARRELL,
JRNL AUTH 2 A.H.WANG
JRNL TITL A NOVEL DNA STRUCTURE INDUCED BY THE ANTICANCER BISPLATINUM
JRNL TITL 2 COMPOUND CROSSLINKED TO A GPC SITE IN DNA.
JRNL REF NAT.STRUCT.BIOL. V. 2 577 1995
JRNL REFN ISSN 1072-8368
JRNL PMID 7664126
JRNL DOI 10.1038/NSB0795-577
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.YANG
REMARK 1 REF THESIS 1996
REMARK 1 PUBL URBANA : UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN (THESIS)
REMARK 1 REFN
REMARK 1 REFERENCE 2
REMARK 1 AUTH D.YANG,A.H.WANG
REMARK 1 TITL STRUCTURAL STUDIES OF INTERACTIONS BETWEEN ANTICANCER
REMARK 1 TITL 2 PLATINUM DRUGS AND DNA
REMARK 1 REF PROG.BIOPHYS.MOL.BIOL. V. 66 81 1996
REMARK 1 REFN ISSN 0079-6107
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: NULL
REMARK 4
REMARK 4 1AU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000171262.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 275
REMARK 210 PH : 7
REMARK 210 IONIC STRENGTH : 150 MM NACL
REMARK 210 PRESSURE : 1 ATM SOLVENT SYSTEM : H2O/D2O
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D1HNOESY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : VXR500
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR, QUANTA
REMARK 210 METHOD USED : NOE-RESTRAINED REFINEMENT
REMARK 210 SPEDREF
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
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: 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
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 H2'' DA A 2 O4' DT A 3 1.56
REMARK 500 H2'' DA B 10 O4' DT B 11 1.56
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 3 C5 DT A 3 C7 0.041
REMARK 500 DG A 4 C8 DG A 4 N9 -0.053
REMARK 500 DC A 5 C5' DC A 5 C4' 0.100
REMARK 500 DC A 5 C5 DC A 5 C6 0.053
REMARK 500 DA A 6 C3' DA A 6 C2' -0.052
REMARK 500 DA A 6 N9 DA A 6 C4 -0.040
REMARK 500 DT A 7 C5 DT A 7 C7 0.044
REMARK 500 DT B 11 C5 DT B 11 C7 0.042
REMARK 500 DG B 12 C8 DG B 12 N9 -0.053
REMARK 500 DC B 13 C5' DC B 13 C4' 0.100
REMARK 500 DC B 13 C5 DC B 13 C6 0.053
REMARK 500 DA B 14 C3' DA B 14 C2' -0.052
REMARK 500 DA B 14 N9 DA B 14 C4 -0.040
REMARK 500 DT B 15 C5 DT B 15 C7 0.043
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 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES
REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DA A 2 C5' - C4' - O4' ANGL. DEV. = 13.0 DEGREES
REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DT A 3 O3' - P - O5' ANGL. DEV. = -12.4 DEGREES
REMARK 500 DT A 3 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DT A 3 C4 - C5 - C7 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.1 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES
REMARK 500 DC A 5 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES
REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DC A 5 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA A 6 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 9.9 DEGREES
REMARK 500 DA A 6 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES
REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 DT A 7 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES
REMARK 500 DG A 8 O4' - C1' - C2' ANGL. DEV. = -8.3 DEGREES
REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 9.7 DEGREES
REMARK 500 DC B 9 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES
REMARK 500 DC B 9 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DA B 10 C5' - C4' - O4' ANGL. DEV. = 13.0 DEGREES
REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DT B 11 O3' - P - O5' ANGL. DEV. = -12.4 DEGREES
REMARK 500 DT B 11 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DT B 11 C4 - C5 - C7 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES
REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG B 12 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG B 12 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES
REMARK 500 DC B 13 C5' - C4' - C3' ANGL. DEV. = 7.4 DEGREES
REMARK 500 DC B 13 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DC B 13 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA B 14 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA B 14 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 DA B 14 O4' - C1' - N9 ANGL. DEV. = 10.0 DEGREES
REMARK 500 DA B 14 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES
REMARK 500 DA B 14 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DT B 15 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES
REMARK 500 DG B 16 O4' - C1' - C2' ANGL. DEV. = -8.3 DEGREES
REMARK 500 DG B 16 O4' - C1' - N9 ANGL. DEV. = 9.7 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 DG A 4 0.10 SIDE CHAIN
REMARK 500 DA A 6 0.07 SIDE CHAIN
REMARK 500 DG B 12 0.10 SIDE CHAIN
REMARK 500 DA B 14 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 BPT A 17 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG A 4 N7
REMARK 620 2 BPT A 17 N1 179.3
REMARK 620 3 BPT A 17 N3 89.2 90.2
REMARK 620 4 BPT A 17 N4 90.9 89.8 179.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 BPT A 17 PT2
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG B 12 N7
REMARK 620 2 BPT A 17 N2 179.2
REMARK 620 3 BPT A 17 N5 89.1 90.1
REMARK 620 4 BPT A 17 N6 90.9 89.8 179.9
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 BPT A 17
DBREF 1AU6 A 1 8 PDB 1AU6 1AU6 1 8
DBREF 1AU6 B 9 16 PDB 1AU6 1AU6 9 16
SEQRES 1 A 8 DC DA DT DG DC DA DT DG
SEQRES 1 B 8 DC DA DT DG DC DA DT DG
HET BPT A 17 36
HETNAM BPT BIS(TRANS-PLATINUM ETHYLENEDIAMINE DIAMINE CHLORO)
HETNAM 2 BPT COMPLEX
HETSYN BPT 1,1/T,T
FORMUL 3 BPT C4 H24 CL2 N6 PT2
LINK N7 DG A 4 PT1 BPT A 17 1555 1555 1.99
LINK PT2 BPT A 17 N7 DG B 12 1555 1555 1.99
SITE 1 AC1 6 DA A 2 DT A 3 DG A 4 DA B 10
SITE 2 AC1 6 DT B 11 DG B 12
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 - 16 202 Bytes