PDB Short entry for 193D 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