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