PDB Short entry for 1CP8 HEADER DNA 11-JUN-99 1CP8 TITLE NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL TITLE 2 ANTITUMOR DRUG UCH9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TWO MOLECULES OF THE DRUG UCH9 (DDA-DXA-DDA-DDL-DRI- COMPND 6 DDA) BOUND IN THE MINOR GROOVE THE MODEL CONTAINS TWO MOLECULES OF COMPND 7 UCH9 AND ONE MG CATION WHICH IS COORDINATED TO TWO UCH9 MOLECULES. IN COMPND 8 THIS ENTRY UCH9 IS PRESENTED AS HET GROUP, DDA-DXA-DDA-DDL-DRI-DDA. COMPND 9 THESE GROUPS ARE NUMBERED 1-6 FOR ONE UCH9 AND 7-12 FOR THE OTHER COMPND 10 UCH9. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA EXPDTA SOLUTION NMR AUTHOR R.KATAHIRA,M.KATAHIRA,Y.YAMASHITA,H.OGAWA,Y.KYOGOKU,M.YOSHIDA REVDAT 4 27-DEC-23 1CP8 1 HETSYN REVDAT 3 29-JUL-20 1CP8 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1CP8 1 VERSN REVDAT 1 01-JUL-99 1CP8 0 JRNL AUTH R.KATAHIRA,M.KATAHIRA,Y.YAMASHITA,H.OGAWA,Y.KYOGOKU, JRNL AUTH 2 M.YOSHIDA JRNL TITL SOLUTION STRUCTURE OF THE NOVEL ANTITUMOR DRUG UCH9 JRNL TITL 2 COMPLEXED WITH D(TTGGCCAA)2 AS DETERMINED BY NMR. JRNL REF NUCLEIC ACIDS RES. V. 26 744 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9443966 JRNL DOI 10.1093/NAR/26.3.744 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. REMARK 3 THE ABSOLUTE CONFIGURATION OF THE HYDROPHILIC SIDECHAIN HAS REMARK 3 NOT BEEN DETERMINED. IN THIS MODEL, IT WAS SET TO THE SAME REMARK 3 CONFIGURATION AS THAT OF THE OTHER AUREOLIC ACID GROUP REMARK 3 COMPOUNDS, SUCH AS CHROMOMYCIN A3. REMARK 4 REMARK 4 1CP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000001176. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY; E.COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: BEST STRUCTURE 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, C, D 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 8 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 3 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG B 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DG B 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA B 7 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 8 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA B 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 14 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DXA A 14 O1 REMARK 620 2 DXA A 14 O9 59.7 REMARK 620 3 DXA B 15 O9 89.4 146.4 REMARK 620 4 DXA B 15 O1 75.2 94.2 63.1 REMARK 620 N 1 2 3 DBREF 1CP8 A 1 8 PDB 1CP8 1CP8 1 8 DBREF 1CP8 B 1 8 PDB 1CP8 1CP8 1 8 SEQRES 1 A 8 DT DT DG DG DC DC DA DA SEQRES 1 B 8 DT DT DG DG DC DC DA DA HET DDA C 1 20 HET DDL C 2 19 HET DRI C 3 22 HET DDA C 4 20 HET DDA D 1 20 HET DDL D 2 19 HET DRI D 3 22 HET DDA D 4 20 HET DDA A 13 21 HET DXA A 14 58 HET DDA B 13 21 HET MG B 14 1 HET DXA B 15 58 HETNAM DDA BETA-D-OLIVOPYRANOSE HETNAM DDL 2,6-DIDEOXY-BETA-D-GALACTOPYRANOSE HETNAM DRI 2,6-DIDEOXY-4-O-METHYL-BETA-D-GLUCOPYRANOSE HETNAM DXA 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4- HETNAM 2 DXA DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-(SEC-BUTYL)- HETNAM 3 DXA ANTHRACENE HETNAM MG MAGNESIUM ION HETSYN DDA BETA-D-OLIVOSE; 2,6-DIDEOXY-BETA-D-ARABINO- HETSYN 2 DDA HEXOPYRANOSE; 2,6-DIDEOXY-BETA-D-GLUCOPYRANOSE; 2,6- HETSYN 3 DDA DIDEOXY-BETA-D-MANNOPYRANOSE; 2-DEOXY-BETA-D- HETSYN 4 DDA QUINOVOPYRANOSE; 2-DEOXY-BETA-D-RHAMNOOPYRANOSE; D- HETSYN 5 DDA OLIVOSE; OLIVOSE; 2,6-DIDEOXY-BETA-D-GLUCOSE; 2,6- HETSYN 6 DDA DIDEOXY-BETA-D-MANNOSE HETSYN DDL 2,6-DIDEOXY-BETA-D-GALACTOSE; 2,6-DIDEOXY-BETA-D- HETSYN 2 DDL TALOSE; 2,6-DIDEOXY-BETA-D-LYXO-HEXOPYRANOSE; 2-DEOXY- HETSYN 3 DDL BETA-D-FUCOPYRANOSE; 2,6-DIDEOXY-D-GALACTOSE; 2,6- HETSYN 4 DDL DIDEOXY-GALACTOSE HETSYN DRI 4-O-METHYL-2,6-DIDEOXY-BETA-D-GLUCOSE; 4-O-METHYL-2,6- HETSYN 2 DRI DIDEOXY-BETA-D-MANNOSE; 2,6-DIDEOXY-4-O-METHYL-BETA-D- HETSYN 3 DRI GLUCOSE; 2,6-DIDEOXY-4-O-METHYL-D-GLUCOSE; 2,6- HETSYN 4 DRI DIDEOXY-4-O-METHYL-GLUCOSE FORMUL 3 DDA 6(C6 H12 O4) FORMUL 3 DDL 2(C6 H12 O4) FORMUL 3 DRI 2(C7 H14 O4) FORMUL 6 DXA 2(C24 H30 O7) FORMUL 8 MG MG 2+ LINK O1 DDA A 13 C6 DXA A 14 1555 1555 1.41 LINK C2 DXA A 14 O1 DDA C 1 1555 1555 1.42 LINK O1 DDA B 13 C6 DXA B 15 1555 1555 1.41 LINK C2 DXA B 15 O1 DDA D 1 1555 1555 1.42 LINK O3 DDA C 1 C1 DDL C 2 1555 1555 1.42 LINK O3 DDL C 2 C1 DRI C 3 1555 1555 1.43 LINK O3 DRI C 3 C1 DDA C 4 1555 1555 1.42 LINK O3 DDA D 1 C1 DDL D 2 1555 1555 1.42 LINK O3 DDL D 2 C1 DRI D 3 1555 1555 1.43 LINK O3 DRI D 3 C1 DDA D 4 1555 1555 1.42 LINK O1 DXA A 14 MG MG B 14 1555 1555 2.75 LINK O9 DXA A 14 MG MG B 14 1555 1555 2.36 LINK MG MG B 14 O9 DXA B 15 1555 1555 2.36 LINK MG MG B 14 O1 DXA B 15 1555 1555 2.54 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