HEADER DNA 09-MAY-03 1P96 TITLE SOLUTION STRUCTURE OF A WEDGE-SHAPED SYNTHETIC MOLECULE AT A TWO-BASE TITLE 2 BULGE SITE IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY DNA SYNTHESIZER.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY DNA SYNTHESIZER. KEYWDS WEDGE-SHAPED SYNTHETIC DRUG-BULGED DNA COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.S.HWANG,G.B.JONES,I.H.GOLDBERG REVDAT 4 23-FEB-22 1P96 1 REMARK REVDAT 3 24-FEB-09 1P96 1 VERSN REVDAT 2 25-MAY-04 1P96 1 HET REVDAT 1 26-AUG-03 1P96 0 JRNL AUTH G.S.HWANG,G.B.JONES,I.H.GOLDBERG JRNL TITL SOLUTION STRUCTURE OF A WEDGE-SHAPED SYNTHETIC MOLECULE AT A JRNL TITL 2 TWO-BASE BULGE SITE IN DNA JRNL REF BIOCHEMISTRY V. 42 8472 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12859193 JRNL DOI 10.1021/BI030072D REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2002.044.17.08, CNS 1.0 REMARK 3 AUTHORS : DELAGLIO, F. (NMRPIPE), BRUNGER, A.T. ET AL (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 694 NOE RESTRANINTS AND 166 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1P96 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019164. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1M NACL, 10MM SODIUM REMARK 210 PHOSPHATE, 0.1MM EDTA REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8MM DDI-BULGED DNA COMPLEX, REMARK 210 0.1M NACL, 10MM SODIUM PHOSPHATE REMARK 210 AND 0.1MM EDTA BUFFER,90% H20/10% REMARK 210 D20; 99.96% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; H REMARK 210 -P COSY; COSY-45 REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.106 REMARK 210 METHOD USED : DISTANCE GEOMETRY SINULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND REMARK 210 HETERONUCLEAR TECHNIQUES. 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDI A 21 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KVH RELATED DB: PDB REMARK 900 THE COMPLEXED STRUCTURE OF THE BULGE DNA AND NATURAL PRODUCT WITH A REMARK 900 SIMILAR AGLYCONE STRUCTURE. DBREF 1P96 A 1 14 PDB 1P96 1P96 1 14 DBREF 1P96 B 1 12 PDB 1P96 1P96 1 12 SEQRES 1 A 14 DC DA DC DG DC DA DG DT DT DC DG DG DA SEQRES 2 A 14 DC SEQRES 1 B 12 DG DT DC DC DG DA DT DG DC DG DT DG HET DDI A 21 70 HETNAM DDI SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2- HETNAM 2 DDI B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D- HETNAM 3 DDI GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R, HETNAM 4 DDI 3'AS,10'AR)-(9CI) FORMUL 3 DDI C31 H31 N O7 SITE 1 AC1 4 DA A 6 DG A 7 DT A 9 DT B 7 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