Header list of 1dsa.pdb file
Complete list - b 16 2 Bytes
HEADER DNA 08-MAY-97 1DSA
TITLE (+)-DUOCARMYCIN SA COVALENTLY LINKED TO DUPLEX DNA, NMR, 20 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3', 5'-
COMPND 3 D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3');
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3', 5'-
COMPND 8 D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3');
COMPND 9 CHAIN: B;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DUOCARMYCIN, DNA, MINOR GROOVE BINDING, ANTITUMOR AGENT, DRUG-DNA
KEYWDS 2 COMPLEX, DEOXYRIBONUCLEIC ACID
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.S.EIS,J.A.SMITH,D.A.CASE,W.J.CHAZIN
REVDAT 3 16-FEB-22 1DSA 1 REMARK LINK
REVDAT 2 24-FEB-09 1DSA 1 VERSN
REVDAT 1 20-AUG-97 1DSA 0
JRNL AUTH P.S.EIS,J.A.SMITH,J.M.RYDZEWSKI,D.A.CASE,D.L.BOGER,
JRNL AUTH 2 W.J.CHAZIN
JRNL TITL HIGH RESOLUTION SOLUTION STRUCTURE OF A DNA DUPLEX ALKYLATED
JRNL TITL 2 BY THE ANTITUMOR AGENT DUOCARMYCIN SA.
JRNL REF J.MOL.BIOL. V. 272 237 1997
JRNL REFN ISSN 0022-2836
JRNL PMID 9299351
JRNL DOI 10.1006/JMBI.1997.1223
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,
REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION.
REMARK 4
REMARK 4 1DSA 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_1000172917.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; 2Q; P.E.
REMARK 210 COSY; 1H-13C HSQC; 1D 31P
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX500; AMX600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NAB, AMBER 4.1
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RESTRAINT VIOLATIONS
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: 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 1 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 2 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 3 DA B 19 N3 DA B 19 C4 0.041
REMARK 500 4 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 5 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 6 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 7 DA B 19 N3 DA B 19 C4 0.041
REMARK 500 8 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 9 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 10 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 11 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 12 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 13 DA B 19 N3 DA B 19 C4 0.038
REMARK 500 14 DA B 19 N3 DA B 19 C4 0.041
REMARK 500 15 DA B 19 N3 DA B 19 C4 0.040
REMARK 500 16 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 17 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 18 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 19 DA B 19 N3 DA B 19 C4 0.039
REMARK 500 20 DA B 19 N3 DA B 19 C4 0.040
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 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.4 DEGREES
REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.1 DEGREES
REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DG B 12 C8 - N9 - C1' ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 DG B 12 C4 - N9 - C1' ANGL. DEV. = -8.4 DEGREES
REMARK 500 1 DC B 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA B 19 N3 - C4 - N9 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.6 DEGREES
REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.3 DEGREES
REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DG B 12 C8 - N9 - C1' ANGL. DEV. = 8.0 DEGREES
REMARK 500 2 DG B 12 C4 - N9 - C1' ANGL. DEV. = -8.2 DEGREES
REMARK 500 2 DC B 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DA B 19 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES
REMARK 500 2 DA B 19 N3 - C4 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 2 DG B 20 C4 - N9 - C1' ANGL. DEV. = -8.1 DEGREES
REMARK 500 2 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DC B 22 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DG A 1 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES
REMARK 500 3 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.7 DEGREES
REMARK 500 3 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 3 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.3 DEGREES
REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 3 DG B 12 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES
REMARK 500 3 DG B 12 C4 - N9 - C1' ANGL. DEV. = -8.4 DEGREES
REMARK 500 3 DC B 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 3 DA B 19 N3 - C4 - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 340 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 DG A 1 0.07 SIDE CHAIN
REMARK 500 1 DC A 3 0.08 SIDE CHAIN
REMARK 500 1 DA A 6 0.13 SIDE CHAIN
REMARK 500 1 DT A 7 0.08 SIDE CHAIN
REMARK 500 1 DT A 8 0.07 SIDE CHAIN
REMARK 500 1 DG A 9 0.06 SIDE CHAIN
REMARK 500 1 DT B 13 0.10 SIDE CHAIN
REMARK 500 1 DC B 14 0.07 SIDE CHAIN
REMARK 500 1 DG B 20 0.10 SIDE CHAIN
REMARK 500 1 DT B 21 0.07 SIDE CHAIN
REMARK 500 2 DG A 1 0.07 SIDE CHAIN
REMARK 500 2 DC A 3 0.08 SIDE CHAIN
REMARK 500 2 DA A 6 0.13 SIDE CHAIN
REMARK 500 2 DT A 7 0.08 SIDE CHAIN
REMARK 500 2 DT A 8 0.08 SIDE CHAIN
REMARK 500 2 DG A 9 0.08 SIDE CHAIN
REMARK 500 2 DT B 13 0.11 SIDE CHAIN
REMARK 500 2 DC B 14 0.07 SIDE CHAIN
REMARK 500 2 DG B 20 0.12 SIDE CHAIN
REMARK 500 2 DT B 21 0.06 SIDE CHAIN
REMARK 500 3 DG A 1 0.06 SIDE CHAIN
REMARK 500 3 DA A 2 0.05 SIDE CHAIN
REMARK 500 3 DC A 3 0.07 SIDE CHAIN
REMARK 500 3 DA A 6 0.13 SIDE CHAIN
REMARK 500 3 DT A 7 0.08 SIDE CHAIN
REMARK 500 3 DT A 8 0.07 SIDE CHAIN
REMARK 500 3 DG A 9 0.09 SIDE CHAIN
REMARK 500 3 DT B 13 0.09 SIDE CHAIN
REMARK 500 3 DC B 14 0.07 SIDE CHAIN
REMARK 500 3 DA B 15 0.05 SIDE CHAIN
REMARK 500 3 DA B 16 0.06 SIDE CHAIN
REMARK 500 3 DG B 20 0.11 SIDE CHAIN
REMARK 500 3 DT B 21 0.07 SIDE CHAIN
REMARK 500 3 DC B 22 0.07 SIDE CHAIN
REMARK 500 4 DG A 1 0.07 SIDE CHAIN
REMARK 500 4 DA A 6 0.11 SIDE CHAIN
REMARK 500 4 DT A 7 0.08 SIDE CHAIN
REMARK 500 4 DT A 8 0.07 SIDE CHAIN
REMARK 500 4 DG A 9 0.09 SIDE CHAIN
REMARK 500 4 DT B 13 0.09 SIDE CHAIN
REMARK 500 4 DC B 14 0.07 SIDE CHAIN
REMARK 500 4 DG B 20 0.12 SIDE CHAIN
REMARK 500 4 DT B 21 0.07 SIDE CHAIN
REMARK 500 4 DC B 22 0.07 SIDE CHAIN
REMARK 500 5 DG A 1 0.07 SIDE CHAIN
REMARK 500 5 DC A 3 0.07 SIDE CHAIN
REMARK 500 5 DA A 6 0.13 SIDE CHAIN
REMARK 500 5 DT A 7 0.09 SIDE CHAIN
REMARK 500 5 DT A 8 0.08 SIDE CHAIN
REMARK 500 5 DG A 9 0.06 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 229 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSA B 23
DBREF 1DSA A 1 11 PDB 1DSA 1DSA 1 11
DBREF 1DSA B 12 22 PDB 1DSA 1DSA 12 22
SEQRES 1 A 11 DG DA DC DT DA DA DT DT DG DA DC
SEQRES 1 B 11 DG DT DC DA DA DT DT DA DG DT DC
HET DSA B 23 59
HETNAM DSA 4-HYDROXY-8-METHYL-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-
HETNAM 2 DSA CARBONYL)-3,6,7,8-TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-
HETNAM 3 DSA CARBOXYLIC ACID METHYL ESTER
HETSYN DSA (+)DUOCARMYCIN SA
FORMUL 3 DSA C25 H25 N3 O7
LINK N3 DA B 19 C13 DSA B 23 1555 1555 1.50
SITE 1 AC1 9 DA A 5 DA A 6 DT A 7 DT A 8
SITE 2 AC1 9 DT B 17 DT B 18 DA B 19 DG B 20
SITE 3 AC1 9 DT B 21
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
Complete list - b 16 2 Bytes