HEADER DNA 11-SEP-02 1MP7 TITLE A THIRD COMPLEX OF POST-ACTIVATED NEOCARZINOSTATIN TITLE 2 CHROMOPHORE WITH DNA. BULGE DNA BINDING FROM THE MINOR TITLE 3 GROOVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*CP*AP*GP*AP*GP*AP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA-DRUG COMPLEX, BULGE DNA, RECOGNITION OF ANTICANCER EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR Y.KWON,Z.XI,L.S.KAPPEN,I.H.GOLDBERG,X.GAO REVDAT 2 24-FEB-09 1MP7 1 VERSN REVDAT 1 18-FEB-03 1MP7 0 JRNL AUTH Y.KWON,Z.XI,L.S.KAPPEN,I.H.GOLDBERG,X.GAO JRNL TITL NEW COMPLEX OF POST-ACTIVATED NEOCARZINOSTATIN JRNL TITL 2 CHROMOPHORE WITH DNA: BULGE DNA BINDING FROM THE JRNL TITL 3 MINOR GROOVE JRNL REF BIOCHEMISTRY V. 42 1186 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12564921 JRNL DOI 10.1021/BI0206210 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : AXEL T. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE CALCULATION WAS BASED REMARK 3 ON A TOTAL OF 316 RESTRAINTS, 258 NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 40 OF DIHEDRAL ANGLE RESTRAINTS, AND 18 DISTANCE REMARK 3 RESTRAINTS FROM HYDROGEN BONDS OF WASON-CREEK BASE PAIRS. REMARK 4 REMARK 4 1MP7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-02. REMARK 100 THE RCSB ID CODE IS RCSB017075. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 268 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE, 0.1 REMARK 210 MM EDTA, PH 6.0; 10 MM SODIUM REMARK 210 PHOSPHATE, 0.1 MM EDTA, PH 6.0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DNA; 10 MM PHOPHATE REMARK 210 BUFFER CONTAINING 0.1 MM EDTA, REMARK 210 PH 6.0; 0.9MM COMPLEX OF NCSI- REMARK 210 GLU-BULGE DNA; 10 MM PHOPHATE REMARK 210 BUFFER CONTAINING 0.1 MM EDTA, REMARK 210 PH 6.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY, REMARK 210 H-P COSY, COSY-45, T1 REMARK 210 MEASUREMENT, TRANSLATIONAL REMARK 210 DIFFUSION CONSTANT MEASUREMENT REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR ASPECT X32, FELIX 98 REMARK 210 AND 2000, X-PLOR 3.851, REMARK 210 MARDIGRAS 3.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED, BACK CALCULATED REMARK 210 DATA AGREE WITH EXPERIMENTAL REMARK 210 NOESY SPECTRUM, STRUCTURES REMARK 210 WITH ACCEPTABLE COVALENT REMARK 210 GEOMETRY, STRUCTURES WITH REMARK 210 FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND HETERONUCLEAR (1H-31P) TECHNIQUES. DIFFUSION REMARK 210 CONSTANT MEASUREMENT EXPERIMENT WAS USED TO ADDRESS THE REMARK 210 CONFORMATION OF THE COMPLEX ADOPTING EITHER HOMODUPLEX OR SELF REMARK 210 -FOLDED HAIRPIN FORM. 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: 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. = 2.9 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 9 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 9 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 214 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 NCG A 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KVH RELATED DB: PDB REMARK 900 1KVH IS THE THE SAME ANTITUMOR ACTIVATED IN THE PRESENCE OF REMARK 900 A THIOL REAGENT AND COMPLEXED WITH VARIOUS DNA SEQUENCE DBREF 1MP7 A 1 10 PDB 1MP7 1MP7 1 10 SEQRES 1 A 10 DG DC DC DA DG DA DG DA DG DC HET NCG A 11 121 HETNAM NCG [(R)-4-((1,3-DIOXOLANE-2-OXY)-4-(S)-YL)-4-HYDROXY]- HETNAM 2 NCG (R)-10-(2-METHYLAMINO-5-METHYL-2,6- HETNAM 3 NCG DIDEOXYGALACTOPYRANOSYL-OXY)-(R)-11-(2-HYDROXY-5- HETNAM 4 NCG METHYL-7-METHOXY-1-NAPHTHOYL-OXY)-(R)-12-S- HETNAM 5 NCG GLUTATHIONYL-4,10,11,12-TETRAHYDROINDACENE HETSYN NCG NCSI-GLU, NEOCARZINOSTATIN-GLUTATHIONE CHROMOPHORE FORMUL 2 NCG C45 H52 N4 O18 S SITE 1 AC1 8 DG A 1 DC A 2 DC A 3 DA A 4 SITE 2 AC1 8 DG A 7 DA A 8 DG A 9 DC A 10 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 156 0 1 0 0 0 2 6 0 0 0 1 END