Header list of 193d.pdb file
Complete list - 1 20 Bytes
HEADER DNA/ANTIBIOTIC 30-SEP-94 193D
TITLE SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: QUINOMYCIN;
COMPND 7 CHAIN: C;
COMPND 8 SYNONYM: QUINOMYCIN A, UK-63052;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 ORGANISM_SCIENTIFIC: STREPTOMYCES;
SOURCE 7 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS BISINTERCALATOR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC,
KEYWDS 2 ANTITUMOR, DNA-ANTIBIOTIC COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR H.CHEN,D.J.PATEL
REVDAT 5 01-NOV-17 193D 1 REMARK ATOM
REVDAT 4 27-JUL-11 193D 1 HETATM REMARK
REVDAT 3 13-JUL-11 193D 1 VERSN
REVDAT 2 24-FEB-09 193D 1 VERSN
REVDAT 1 27-FEB-95 193D 0
JRNL AUTH H.CHEN,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA
JRNL TITL 2 COMPLEX.
JRNL REF J.MOL.BIOL. V. 246 164 1995
JRNL REFN ISSN 0022-2836
JRNL PMID 7853395
JRNL DOI 10.1006/JMBI.1994.0074
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: TWO STARTING STRUCTURES WERE GENERATED
REMARK 3 BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING
REMARK 3 INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED
REMARK 3 MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE
REMARK 3 RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS
REMARK 3 WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-
REMARK 3 REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-
REMARK 3 MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE
REMARK 3 FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE
REMARK 3 COORDINATES OF THE LAST 0.5 PS OF THE DYNAMICS DURING RELAXATION
REMARK 3 MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS
REMARK 3 USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX
REMARK 3 REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED,
REMARK 3 QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND
REMARK 3 MIXING TIMES OF 30, 60, 120 AND 180 MS. THE R(1/6) FACTOR AND
REMARK 3 THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL
REMARK 3 STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.023
REMARK 3 0.024 0.024 0.026 BOND (ANG) 0.011 0.011 0.011 0.011 ANGLES (DEG)
REMARK 3 3.616 3.657 3.700 3.725 IMPROPERS (DEG) 0.274 0.285 0.241 0.298
REMARK 4
REMARK 4 193D 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_1000170207.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX
REMARK 210 RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 4
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 400
REMARK 400 COMPOUND
REMARK 400 QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE,
REMARK 400 A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS.
REMARK 400 HERE, QUINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
REMARK 400 SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) HQU
REMARK 400
REMARK 400 THE UK63052 IS CYCLIC DEPSIPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: UK63052
REMARK 400 CHAIN: C
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 COMPONENT_2: RESIDUE HQU, 2 COPIES
REMARK 400 DESCRIPTION: QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE.
REMARK 400 BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE
REMARK 400 C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3
REMARK 400 AND 7. THE TWO HYDROXYQUINOXALINE CHROMOPHORES ARE
REMARK 400 LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
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 A 1 C8 DA A 1 N9 -0.048
REMARK 500 1 DT A 8 C5 DT A 8 C7 0.040
REMARK 500 1 DT B 6 C5 DT B 6 C7 0.041
REMARK 500 1 DT B 8 C5 DT B 8 C7 0.039
REMARK 500 2 DA A 1 C8 DA A 1 N9 -0.049
REMARK 500 2 DA B 1 C8 DA B 1 N9 -0.048
REMARK 500 2 DT B 6 C5 DT B 6 C7 0.037
REMARK 500 2 DT B 8 C5 DT B 8 C7 0.038
REMARK 500 3 DA A 1 C8 DA A 1 N9 -0.050
REMARK 500 3 DT A 8 C5 DT A 8 C7 0.040
REMARK 500 3 DA B 1 C8 DA B 1 N9 -0.049
REMARK 500 3 DT B 8 C5 DT B 8 C7 0.041
REMARK 500 4 DA A 1 C8 DA A 1 N9 -0.053
REMARK 500 4 DA B 1 C8 DA B 1 N9 -0.051
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 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES
REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DA B 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DC B 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DC B 2 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 DC B 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DC B 4 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DT B 6 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DC A 2 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES
REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DA B 1 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES
REMARK 500 2 DA B 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DC B 2 C5' - C4' - C3' ANGL. DEV. = 7.2 DEGREES
REMARK 500 2 DC B 2 O4' - C1' - N1 ANGL. DEV. = -4.3 DEGREES
REMARK 500 2 DC B 2 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES
REMARK 500 2 DA B 3 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 DC B 4 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 2 DC B 4 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG B 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG B 7 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DG B 7 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 3 DA A 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 DA A 1 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES
REMARK 500 3 DA A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = -4.7 DEGREES
REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 101 ANGLE 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 CHAIN C OF QUINOMYCIN
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 185D RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A
REMARK 900 RELATED ID: 1PFE RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP P6322
REMARK 900 RELATED ID: 1VS2 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A
REMARK 900 RELATED ID: 1XVK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP P632
REMARK 900 RELATED ID: 1XVN RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP P632
REMARK 900 RELATED ID: 1XVR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP C21
REMARK 900 RELATED ID: 2ADW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP P42212
REMARK 900 RELATED ID: 2DA8 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN
REMARK 900 A AT POSITIONS 4 AND 8
REMARK 900 RELATED ID: 3GO3 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE
REMARK 900 GROUP P41212
DBREF 193D A 1 8 PDB 193D 193D 1 8
DBREF 193D B 1 8 PDB 193D 193D 1 8
DBREF 193D C 1 8 PDB 193D 193D 1 8
SEQRES 1 A 8 DA DC DA DC DG DT DG DT
SEQRES 1 B 8 DA DC DA DC DG DT DG DT
SEQRES 1 C 8 DSN ALA NYB CPC DSN ALA NCY CPC
HET DSN C 1 10
HET NYB C 3 25
HET CPC C 4 17
HET DSN C 5 10
HET NCY C 7 13
HET CPC C 8 17
HET HQU C 0 19
HET HQU C 9 19
HETNAM DSN D-SERINE
HETNAM NYB N-METHYL-S-[(1R)-1-METHYLPROPYL]-L-CYSTEINE
HETNAM CPC 2-METHYL-1-METHYLAMINO-CYCLOPROPANE CARBOXYLIC ACID
HETNAM NCY N-METHYLCYSTEINE
HETNAM HQU 3-HYDROXYQUINALDIC ACID
FORMUL 3 DSN 2(C3 H7 N O3)
FORMUL 3 NYB C8 H17 N O2 S
FORMUL 3 CPC 2(C6 H11 N O2)
FORMUL 3 NCY C4 H9 N O2 S
FORMUL 4 HQU 2(C10 H7 N O3)
LINK C HQU C 0 N DSN C 1 1555 1555 1.31
LINK C DSN C 1 N ALA C 2 1555 1555 1.31
LINK OG DSN C 1 C CPC C 8 1555 1555 1.39
LINK C ALA C 2 N NYB C 3 1555 1555 1.33
LINK CB NYB C 3 SG NCY C 7 1555 1555 1.81
LINK C NYB C 3 N CPC C 4 1555 1555 1.33
LINK C CPC C 4 OG DSN C 5 1555 1555 1.39
LINK C DSN C 5 N ALA C 6 1555 1555 1.31
LINK N DSN C 5 C HQU C 9 1555 1555 1.31
LINK C ALA C 6 N NCY C 7 1555 1555 1.33
LINK C NCY C 7 N CPC C 8 1555 1555 1.33
SITE 1 AC1 8 DA A 3 DC A 4 DG A 5 DT A 6
SITE 2 AC1 8 DA B 3 DC B 4 DG B 5 DT B 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
MODEL 1
Complete list - 1 20 Bytes