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 6 22-MAY-24 1DSI 1 REMARK 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