Header list of 1dsi.pdb file
Complete list - b 16 2 Bytes
HEADER DNA 29-JUL-98 1DSI
TITLE SOLUTION STRUCTURE OF A DUOCARMYCIN SA-INDOLE-ALKYLATED DNA DUPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*CP*TP*AP*AP*TP*TP*GP*AP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: MINOR GROOVE BOUND DUOCARMYCIN SA-INDOLE;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*AP*TP*TP*AP*GP*TP*C)-3');
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: MINOR GROOVE BOUND DUOCARMYCIN SA-INDOLE
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DEOXYRIBONUCLEIC ACID, DUOCARMYCIN, DNA, MINOR GROOVE BINDING,
KEYWDS 2 ANTITUMOR AGENT, LIGAND-DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.R.SCHNELL,R.R.KETCHEM,D.L.BOGER,W.J.CHAZIN
REVDAT 5 16-FEB-22 1DSI 1 REMARK LINK
REVDAT 4 24-FEB-09 1DSI 1 VERSN
REVDAT 3 19-APR-05 1DSI 1 JRNL REMARK HETNAM MASTER
REVDAT 2 22-DEC-99 1DSI 4 HEADER COMPND REMARK JRNL
REVDAT 2 2 4 ATOM SOURCE SEQRES
REVDAT 1 05-AUG-98 1DSI 0
JRNL AUTH J.R.SCHNELL,R.R.KETCHEM,D.L.BOGER,W.J.CHAZIN
JRNL TITL BINDING-INDUCED ACTIVATION OF DNA ALKYLATION BY DUOCARMYCIN
JRNL TITL 2 SA: INSIGHTS FROM THE STRUCTURE OF AN INDOLE DERIVATIVE-DNA
JRNL TITL 3 ADDUCT
JRNL REF J.AM.CHEM.SOC. V. 121 5645 1999
JRNL REFN ISSN 0002-7863
JRNL DOI 10.1021/JA983556J
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH P.S.EIS,J.A.SMITH,J.M.RYDZEWSKI,D.A.CASE,D.L.BOGER,
REMARK 1 AUTH 2 W.J.CHAZIN
REMARK 1 TITL HIGH RESOLUTION SOLUTION STRUCTURE OF A DNA DUPLEX ALKYLATED
REMARK 1 TITL 2 BY THE ANTITUMOR AGENT DUOCARMYCIN SA
REMARK 1 REF J.MOL.BIOL. V. 272 237 1997
REMARK 1 REFN ISSN 0022-2836
REMARK 1 REFERENCE 2
REMARK 1 AUTH D.L.BOGER,D.L.HERZOG,B.BOLLINGER,D.S.JOHNSON,H.CAI,
REMARK 1 AUTH 2 J.GOLDBERG,P.TURNBULL
REMARK 1 TITL DUOCARMYCIN SA SHORTENED, SIMPLIFIED, AND EXTENDED AGENTS: A
REMARK 1 TITL 2 SYSTEMATIC EXAMINATION OF THE ROLE OF THE DNA BINDING
REMARK 1 TITL 3 SUBUNIT
REMARK 1 REF J.AM.CHEM.SOC. V. 119 4977 1997
REMARK 1 REFN ISSN 0002-7863
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 5.1
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 ABOVE.
REMARK 4
REMARK 4 1DSI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB.
REMARK 100 THE DEPOSITION ID IS D_1000008178.
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 : 150MM
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 : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 97, NAB 2.1, MARDIGRAS
REMARK 210 5.21, AMBER 5.1
REMARK 210 METHOD USED : NAB TO GENERATE A FAMILY OF
REMARK 210 CONFOMRERS THAT SAMPLE A WIDE
REMARK 210 RANGE OF CONFORMATIONAL SPACE.
REMARK 210 RESTRAINED MOLECULAR DYNAMICS TO
REMARK 210 GENERATE A RANGE OF STARTING
REMARK 210 STRUCTURES FOR DSI. PAIRS OF DNA
REMARK 210 AND DSI STRUCTURES WERE THEN
REMARK 210 DOCKED AND ITERATIVELY REFINED
REMARK 210 BY A SERIES OF RESTRAINED
REMARK 210 MOLECULAR DYNAMICS CALCULATIONS.
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 : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H NMR DATA.
REMARK 210 RESONANCE
REMARK 210 ASSIGNMENTS WERE AIDED BY A 1H - 13C HSQC EXPERIMENT PERFORMED AT
REMARK 210 NATURAL
REMARK 210 ISOTOPE ABUNDANCE.
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 3 DA B 19 N3 DA B 19 C4 0.036
REMARK 500 7 DA B 19 N3 DA B 19 C4 0.037
REMARK 500 8 DA B 19 N3 DA B 19 C4 0.037
REMARK 500 9 DA B 19 N3 DA B 19 C4 0.036
REMARK 500 12 DA B 19 N3 DA B 19 C4 0.036
REMARK 500 13 DA B 19 N3 DA B 19 C4 0.036
REMARK 500 14 DA B 19 N3 DA B 19 C4 0.036
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. = 2.8 DEGREES
REMARK 500 1 DG A 1 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.8 DEGREES
REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.3 DEGREES
REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.4 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. = 2.9 DEGREES
REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 2 DG A 1 C8 - N9 - C1' ANGL. DEV. = 8.1 DEGREES
REMARK 500 2 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.9 DEGREES
REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.2 DEGREES
REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 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. = -8.3 DEGREES
REMARK 500 2 DC B 14 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.9 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. = 7.8 DEGREES
REMARK 500 3 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.7 DEGREES
REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 3 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.5 DEGREES
REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 3 DG B 12 C8 - N9 - C1' ANGL. DEV. = 8.2 DEGREES
REMARK 500 3 DG B 12 C4 - N9 - C1' ANGL. DEV. = -8.6 DEGREES
REMARK 500 3 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 3 DT B 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 DA B 19 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 3 DT B 21 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 3 DC B 22 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 4 DG A 1 C4 - N9 - C1' ANGL. DEV. = -8.8 DEGREES
REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 4 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 4 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 4 DG A 9 C4 - N9 - C1' ANGL. DEV. = -8.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 314 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 0.10 SIDE CHAIN
REMARK 500 1 DA A 6 0.10 SIDE CHAIN
REMARK 500 1 DT A 7 0.07 SIDE CHAIN
REMARK 500 1 DT A 8 0.06 SIDE CHAIN
REMARK 500 1 DT B 13 0.09 SIDE CHAIN
REMARK 500 1 DC B 14 0.07 SIDE CHAIN
REMARK 500 1 DA B 19 0.11 SIDE CHAIN
REMARK 500 1 DG B 20 0.09 SIDE CHAIN
REMARK 500 1 DT B 21 0.06 SIDE CHAIN
REMARK 500 1 DC B 22 0.07 SIDE CHAIN
REMARK 500 2 DA A 2 0.08 SIDE CHAIN
REMARK 500 2 DA A 6 0.12 SIDE CHAIN
REMARK 500 2 DT A 7 0.06 SIDE CHAIN
REMARK 500 2 DT A 8 0.08 SIDE CHAIN
REMARK 500 2 DG A 9 0.07 SIDE CHAIN
REMARK 500 2 DT B 13 0.09 SIDE CHAIN
REMARK 500 2 DC B 14 0.07 SIDE CHAIN
REMARK 500 2 DT B 17 0.06 SIDE CHAIN
REMARK 500 2 DA B 19 0.10 SIDE CHAIN
REMARK 500 2 DG B 20 0.08 SIDE CHAIN
REMARK 500 3 DA A 2 0.10 SIDE CHAIN
REMARK 500 3 DA A 6 0.11 SIDE CHAIN
REMARK 500 3 DT A 7 0.07 SIDE CHAIN
REMARK 500 3 DT A 8 0.08 SIDE CHAIN
REMARK 500 3 DG A 9 0.06 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 19 0.09 SIDE CHAIN
REMARK 500 3 DG B 20 0.09 SIDE CHAIN
REMARK 500 4 DG A 1 0.06 SIDE CHAIN
REMARK 500 4 DA A 2 0.10 SIDE CHAIN
REMARK 500 4 DA A 6 0.10 SIDE CHAIN
REMARK 500 4 DT A 8 0.08 SIDE CHAIN
REMARK 500 4 DG A 9 0.07 SIDE CHAIN
REMARK 500 4 DT B 13 0.08 SIDE CHAIN
REMARK 500 4 DC B 14 0.06 SIDE CHAIN
REMARK 500 4 DA B 19 0.10 SIDE CHAIN
REMARK 500 4 DG B 20 0.10 SIDE CHAIN
REMARK 500 4 DT B 21 0.06 SIDE CHAIN
REMARK 500 5 DA A 2 0.09 SIDE CHAIN
REMARK 500 5 DA A 6 0.10 SIDE CHAIN
REMARK 500 5 DT A 7 0.08 SIDE CHAIN
REMARK 500 5 DT A 8 0.07 SIDE CHAIN
REMARK 500 5 DT B 13 0.08 SIDE CHAIN
REMARK 500 5 DC B 14 0.07 SIDE CHAIN
REMARK 500 5 DA B 19 0.11 SIDE CHAIN
REMARK 500 5 DG B 20 0.08 SIDE CHAIN
REMARK 500 5 DT B 21 0.07 SIDE CHAIN
REMARK 500 6 DA A 2 0.08 SIDE CHAIN
REMARK 500 6 DA A 6 0.11 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 205 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 DSI B 23
DBREF 1DSI A 1 11 PDB 1DSI 1DSI 1 11
DBREF 1DSI B 12 22 PDB 1DSI 1DSI 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 DSI B 23 47
HETNAM DSI 4-HYDROXY-6-(1H-INDOLE-2-CARBONYL)-8-METHYL-3,6,7,8-
HETNAM 2 DSI TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID
HETNAM 3 DSI METHYL ESTER
HETSYN DSI (+)DUOCARMYCIN SA-INDOLE
FORMUL 3 DSI C22 H19 N3 O4
LINK N3 DA B 19 C13 DSI B 23 1555 1555 1.49
SITE 1 AC1 7 DA A 5 DA A 6 DT A 7 DT B 18
SITE 2 AC1 7 DA B 19 DG B 20 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