10 20 30 40 50 60 70 80 1CP8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 11-JUN-99 1CP8
TITLE NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH TITLE 2 NOVEL 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- COMPND 6 DDL-DRI-DDA) BOUND IN THE MINOR GROOVE THE MODEL CONTAINS COMPND 7 TWO MOLECULES OF UCH9 AND ONE MG CATION WHICH IS COMPND 8 COORDINATED TO TWO UCH9 MOLECULES. IN THIS ENTRY UCH9 IS COMPND 9 PRESENTED AS HET GROUP, DDA-DXA-DDA-DDL-DRI-DDA. THESE COMPND 10 GROUPS ARE NUMBERED 1-6 FOR ONE UCH9 AND 7-12 FOR COMPND 11 THE OTHER 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, AUTHOR 2 M.YOSHIDA
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, JRNL AUTH 2 Y.KYOGOKU,M.YOSHIDA JRNL TITL SOLUTION STRUCTURE OF THE NOVEL ANTITUMOR DRUG JRNL TITL 2 UCH9 COMPLEXED WITH D(TTGGCCAA)2 AS DETERMINED BY JRNL TITL 3 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 1
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: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE. THE ABSOLUTE CONFIGURATION OF THE REMARK 3 HYDROPHILIC SIDECHAIN HAS NOT BEEN DETERMINED. IN THIS MODEL, REMARK 3 IT WAS SET TO THE SAME CONFIGURATION AS THAT OF THE OTHER REMARK 3 AUREOLIC ACID GROUP COMPOUNDS, SUCH AS CHROMOMYCIN A3.
REMARK 4 REMARK 4 1CP8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB001176.
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 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. = 3.4 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DDA B 9 REMARK 610 DDL B 10 REMARK 610 DDA B 12 REMARK 610 DDA A 9 REMARK 610 DDL A 10 REMARK 610 DDA A 12
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 B 15 O9 89.4 REMARK 620 3 DXA B 15 O1 75.2 63.1 REMARK 620 4 DXA A 14 O9 59.7 146.4 94.2 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 9 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDL B 10 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DRI B 11 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 12 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 9 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDL A 10 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DRI A 11 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 12 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 13 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA A 13 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 14 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXA B 15 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DXA A 14
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 B 9 19 HET DDL B 10 19 HET DRI B 11 23 HET DDA B 12 20 HET DDA A 9 19 HET DDL A 10 19 HET DRI A 11 23 HET DDA A 12 20 HET DDA B 13 21 HET DDA A 13 21 HET MG B 14 1 HET DXA B 15 58 HET DXA A 14 58
HETNAM DDA 2,6-DIDEOXY-BETA-D-GLUCOSE HETNAM DDL 2,6-DIDEOXY-BETA-D-GALACTOSE HETNAM DRI 4-O-METHYL-2,6-DIDEOXY-BETA-D-GLUCOSE HETNAM MG MAGNESIUM ION 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
HETSYN DDA 2,6-DIDEOXY-BETA-D-MANNOSE HETSYN DDL 2,6-DIDEOXY-BETA-D-TALOSE HETSYN DRI 4-O-METHYL-2,6-DIDEOXY-BETA-D-MANNOSE
FORMUL 3 DDA 6(C6 H12 O4) FORMUL 3 DDL 2(C6 H12 O4) FORMUL 3 DRI 2(C7 H14 O4) FORMUL 7 MG MG 2+ FORMUL 8 DXA 2(C24 H30 O7)
LINK C3 DDA B 9 O1 DDL B 10 1555 1555 1.42 LINK C3 DDL B 10 O1 DRI B 11 1555 1555 1.43 LINK O3 DRI B 11 C1 DDA B 12 1555 1555 1.42 LINK C3 DDA A 9 O1 DDL A 10 1555 1555 1.42 LINK C3 DDL A 10 O1 DRI A 11 1555 1555 1.43 LINK O3 DRI A 11 C1 DDA A 12 1555 1555 1.42 LINK O1 DDA B 13 C6 DXA B 15 1555 1555 1.41 LINK O1 DDA A 13 C6 DXA A 14 1555 1555 1.41 LINK O1 DDA B 9 C2 DXA B 15 1555 1555 1.42 LINK O1 DDA A 9 C2 DXA A 14 1555 1555 1.42 LINK MG MG B 14 O1 DXA A 14 1555 1555 2.75 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 LINK MG MG B 14 O9 DXA A 14 1555 1555 2.36
SITE 1 AC1 3 DC B 6 DDL B 10 DXA B 15 SITE 1 AC2 4 DDA A 13 DA B 7 DDA B 9 DRI B 11 SITE 1 AC3 5 DDA A 13 DXA A 14 DA B 8 DDL B 10 SITE 2 AC3 5 DDA B 12 SITE 1 AC4 4 DT A 2 DA B 7 DA B 8 DRI B 11 SITE 1 AC5 3 DC A 6 DDL A 10 DXA A 14 SITE 1 AC6 5 DA A 7 DDA A 9 DRI A 11 DDA B 13 SITE 2 AC6 5 DXA B 15 SITE 1 AC7 5 DA A 8 DDL A 10 DDA A 12 DDA B 13 SITE 2 AC7 5 DXA B 15 SITE 1 AC8 4 DA A 7 DA A 8 DRI A 11 DT B 2 SITE 1 AC9 3 DDL A 10 DRI A 11 DXA B 15 SITE 1 BC1 3 DXA A 14 DDL B 10 DRI B 11 SITE 1 BC2 4 DC A 5 DXA A 14 DC B 5 DXA B 15 SITE 1 BC3 11 DA A 7 DDL A 10 DRI A 11 DXA A 14 SITE 2 BC3 11 DG B 4 DC B 5 DC B 6 DA B 7 SITE 3 BC3 11 DDA B 9 DDA B 13 MG B 14 SITE 1 BC4 10 DG A 4 DC A 5 DC A 6 DA A 7 SITE 2 BC4 10 DDA A 9 DDA A 13 DA B 7 DRI B 11 SITE 3 BC4 10 MG B 14 DXA B 15
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