HEADER DNA 17-JAN-95 107D TITLE SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 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 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, NMR, DOUBLE HELIX EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR C.H.LIN,D.J.PATEL REVDAT 3 07-APR-09 107D 1 REMARK REVDAT 2 24-FEB-09 107D 1 VERSN REVDAT 1 08-MAY-95 107D 0 JRNL AUTH C.H.LIN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN JRNL TITL 2 A-DNA DUPLEX COMPLEX. JRNL REF J.MOL.BIOL. V. 248 162 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7731041 JRNL DOI 10.1006/JMBI.1995.0209 REMARK 1 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 REMARK 3 GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA REMARK 3 USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- REMARK 3 RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON REMARK 3 DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL REMARK 3 VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH REMARK 3 YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED REMARK 3 FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX REMARK 3 BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE REMARK 3 THE FINAL FOUR STRUCTURES. THE FINAL FOUR STRUCTURES WERE REMARK 3 OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS REMARK 3 OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY REMARK 3 MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE REMARK 3 DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN REMARK 3 THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY REMARK 3 SPECTRA RECORDED IN D2O AND MIXING TIMES OF 40, 80, 120 AND REMARK 3 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL REMARK 3 GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/ REMARK 3 6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) REMARK 3 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS REMARK 3 APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE REMARK 3 DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. REMARK 3 THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED REMARK 3 STRUCTURE OF THE FOUR MODELS. REMARK 4 REMARK 4 107D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., REMARK 210 JAPAN. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N3 DA B 12 C10 DUO B 15 1.41 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 5 C5 DT A 5 C7 0.041 REMARK 500 2 DT A 3 C5 DT A 3 C7 0.038 REMARK 500 2 DT A 4 C5 DT A 4 C7 0.037 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.048 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 4 DT A 3 C5 DT A 3 C7 0.040 REMARK 500 4 DT A 5 C5 DT A 5 C7 0.039 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 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA B 12 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 3 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG B 13 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 3 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 4 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA B 12 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 3 DA B 12 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DG B 13 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 4 DC A 1 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DT A 3 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 DA B 9 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 DG B 8 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 4 DA B 10 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 DA B 9 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 55 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 RESIDUE DUO B 15 DBREF 107D A 1 7 PDB 107D 107D 1 7 DBREF 107D B 8 14 PDB 107D 107D 8 14 SEQRES 1 A 7 DC DC DT DT DT DT DC SEQRES 1 B 7 DG DA DA DA DA DG DG HET DUO B 15 63 HETNAM DUO 4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H- HETNAM 2 DUO INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS- HETNAM 3 DUO INDACENE-2-CARBOXYLIC ACID METHYL ESTER HETSYN DUO DUOCARMYCIN A FORMUL 3 DUO C26 H27 N3 O8 SITE 1 AC1 9 DT A 4 DT A 5 DT A 6 DC A 7 SITE 2 AC1 9 DA B 10 DA B 11 DA B 12 DG B 13 SITE 3 AC1 9 DG B 14 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 ENDMDL ENDMDL ENDMDL ENDMDL MASTER 179 0 1 0 0 0 3 6 0 0 0 2 END