HEADER DNA 12-NOV-98 1B0S TITLE BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE BINDER, TO CCGG TITLE 2 SEQUENCE ANALYZED BY NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*AP*CP*CP*GP*GP*TP*TP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ANTICANCER DRUG, DRUG DESIGN, DNA STRUCTURE, SEQUENCE SPECIFIC KEYWDS 2 RECOGNITION, DNA EXPDTA SOLUTION NMR AUTHOR X.-L.YANG,C.KAENZIG,M.LEE,A.H.-J.WANG REVDAT 5 27-DEC-23 1B0S 1 REMARK REVDAT 4 16-FEB-22 1B0S 1 COMPND REMARK HETNAM REVDAT 3 24-FEB-09 1B0S 1 VERSN REVDAT 2 01-APR-03 1B0S 1 JRNL REVDAT 1 31-AUG-99 1B0S 0 JRNL AUTH X.L.YANG,C.KAENZIG,M.LEE,A.H.WANG JRNL TITL BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE JRNL TITL 2 BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY. JRNL REF EUR.J.BIOCHEM. V. 263 646 1999 JRNL REFN ISSN 0014-2956 JRNL PMID 10469127 JRNL DOI 10.1046/J.1432-1327.1999.00515.X 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: NULL REMARK 4 REMARK 4 1B0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000001228. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY 750; VXR 500 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1, SPEDREF REMARK 210 METHOD USED : NOE-RMD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REFINED AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 REFINED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING 1H REMARK 210 2D NMR REMARK 210 SPECTROSCOPY 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT A 8 C5 DT A 8 C7 0.048 REMARK 500 DT A 9 C5 DT A 9 C7 0.050 REMARK 500 DC A 10 C5 DC A 10 C6 0.049 REMARK 500 DT B 18 C5 DT B 18 C7 0.048 REMARK 500 DT B 19 C5 DT B 19 C7 0.049 REMARK 500 DC B 20 C5 DC B 20 C6 0.050 REMARK 500 REMARK 500 REMARK: NULL 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 6 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC A 10 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 13 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC B 15 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC B 15 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 16 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 DC B 20 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DT A 8 0.07 SIDE CHAIN REMARK 500 DT A 9 0.07 SIDE CHAIN REMARK 500 DT B 19 0.07 SIDE CHAIN 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 AR1 A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AR1 B 2 DBREF 1B0S A 1 10 PDB 1B0S 1B0S 1 10 DBREF 1B0S B 11 20 PDB 1B0S 1B0S 11 20 SEQRES 1 A 10 DG DA DA DC DC DG DG DT DT DC SEQRES 1 B 10 DG DA DA DC DC DG DG DT DT DC HET AR1 A 11 63 HET AR1 B 2 63 HETNAM AR1 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2- HETNAM 2 AR1 CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}- HETNAM 3 AR1 AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}- HETNAM 4 AR1 ETHYL)-DIMETHYL-AMMONIUM HETSYN AR1 TRI-IMIDAZOLE DNA MINOR GROOVE BINDER; AR-1-144 FORMUL 3 AR1 2(C20 H28 N11 O4 1+) SITE 1 AC1 9 DC A 5 DG A 6 DG A 7 DT A 8 SITE 2 AC1 9 DT A 9 AR1 B 2 DC B 14 DG B 16 SITE 3 AC1 9 DG B 17 SITE 1 AC2 9 DC A 4 DG A 6 DG A 7 AR1 A 11 SITE 2 AC2 9 DC B 15 DG B 16 DG B 17 DT B 18 SITE 3 AC2 9 DT B 19 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