PDB Short entry for 1MP7 HEADER DNA 11-SEP-02 1MP7 TITLE A THIRD COMPLEX OF POST-ACTIVATED NEOCARZINOSTATIN CHROMOPHORE WITH TITLE 2 DNA. BULGE DNA BINDING FROM THE MINOR 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, DNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR Y.KWON,Z.XI,L.S.KAPPEN,I.H.GOLDBERG,X.GAO REVDAT 3 23-FEB-22 1MP7 1 REMARK HETSYN 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 CHROMOPHORE JRNL TITL 2 WITH DNA: BULGE DNA BINDING FROM THE MINOR GROOVE JRNL REF BIOCHEMISTRY V. 42 1186 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12564921 JRNL DOI 10.1021/BI0206210 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR ASPECT X32, X-PLOR 3.851 REMARK 3 AUTHORS : BRUKER (UXNMR), AXEL T. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE CALCULATION WAS BASED ON A TOTAL OF 316 RESTRAINTS, REMARK 3 258 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 40 OF DIHEDRAL ANGLE RESTRAINTS, AND 18 REMARK 3 DISTANCE RESTRAINTS REMARK 3 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 13-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017075. 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 MM REMARK 210 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 BUFFER REMARK 210 CONTAINING 0.1 MM EDTA, PH 6.0; REMARK 210 0.9MM COMPLEX OF NCSI-GLU-BULGE REMARK 210 DNA; 10 MM PHOPHATE BUFFER REMARK 210 CONTAINING 0.1 MM EDTA, PH 6.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; H REMARK 210 -P COSY, COSY-45, T1 MEASUREMENT, REMARK 210 TRANSLATIONAL DIFFUSION REMARK 210 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 : FELIX 98 AND 2000, X-PLOR 3.851, REMARK 210 MARDIGRAS 3.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, RESTRAINED MOLECULAR REMARK 210 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 DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM, STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR AND REMARK 210 HETERONUCLEAR (1H-31P) TECHNIQUES. REMARK 210 DIFFUSION 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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. = 3.0 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. = 3.5 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 A THIOL REMARK 900 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]-(R)- HETNAM 2 NCG 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