Header list of 107d.pdb file
Complete list - 16 20 Bytes
HEADER DNA 17-JAN-95 107D
TITLE SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3');
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 4 MOL_ID: 2;
SOURCE 5 SYNTHETIC: YES;
SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, DOUBLE HELIX
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR C.H.LIN,D.J.PATEL
REVDAT 4 16-FEB-22 107D 1 REMARK
REVDAT 3 07-APR-09 107D 1 REMARK
REVDAT 2 24-FEB-09 107D 1 VERSN
REVDAT 1 08-MAY-95 107D 0
JRNL AUTH C.H.LIN,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX
JRNL TITL 2 COMPLEX.
JRNL REF J.MOL.BIOL. V. 248 162 1995
JRNL REFN ISSN 0022-2836
JRNL PMID 7731041
JRNL DOI 10.1006/JMBI.1995.0209
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: TWO STARTING STRUCTURES WERE GENERATED
REMARK 3 BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING
REMARK 3 INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED
REMARK 3 MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE
REMARK 3 RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL VELOCITY
REMARK 3 SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO
REMARK 3 DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO
REMARK 3 INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-
REMARK 3 RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR
REMARK 3 STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING
REMARK 3 THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS
REMARK 3 DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE
REMARK 3 R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION
REMARK 3 MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED,
REMARK 3 QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND
REMARK 3 MIXING TIMES OF 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND
REMARK 3 THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL
REMARK 3 STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND
REMARK 3 (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-
REMARK 3 0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING
REMARK 3 THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR
REMARK 3 TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED
REMARK 3 FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS.
REMARK 4
REMARK 4 107D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170017.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX
REMARK 210 RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO.,
REMARK 210 JAPAN.
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 N3 DA B 12 C10 DUO B 15 1.41
REMARK 500
REMARK 500 REMARK: NULL
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 1 DT A 5 C5 DT A 5 C7 0.041
REMARK 500 2 DT A 3 C5 DT A 3 C7 0.038
REMARK 500 2 DT A 4 C5 DT A 4 C7 0.037
REMARK 500 2 DT A 5 C5 DT A 5 C7 0.048
REMARK 500 2 DT A 6 C5 DT A 6 C7 0.036
REMARK 500 4 DT A 3 C5 DT A 3 C7 0.040
REMARK 500 4 DT A 5 C5 DT A 5 C7 0.039
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 1 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.3 DEGREES
REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DT A 4 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 DA B 12 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DT A 3 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 DG B 13 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES
REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 3 DT A 4 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES
REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DA B 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DA B 12 O4' - C1' - C2' ANGL. DEV. = -6.4 DEGREES
REMARK 500 3 DA B 12 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 3 DG B 13 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 3 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 4 DC A 1 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 4 DT A 3 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES
REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES
REMARK 500 4 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 4 DG B 8 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 4 DA B 9 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500 4 DA B 9 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES
REMARK 500 4 DA B 10 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 55 ANGLE DEVIATIONS.
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 DUO B 15
DBREF 107D A 1 7 PDB 107D 107D 1 7
DBREF 107D B 8 14 PDB 107D 107D 8 14
SEQRES 1 A 7 DC DC DT DT DT DT DC
SEQRES 1 B 7 DG DA DA DA DA DG DG
HET DUO B 15 63
HETNAM DUO 4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-
HETNAM 2 DUO INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-
HETNAM 3 DUO INDACENE-2-CARBOXYLIC ACID METHYL ESTER
HETSYN DUO DUOCARMYCIN A
FORMUL 3 DUO C26 H27 N3 O8
SITE 1 AC1 9 DT A 4 DT A 5 DT A 6 DC A 7
SITE 2 AC1 9 DA B 10 DA B 11 DA B 12 DG B 13
SITE 3 AC1 9 DG B 14
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
Complete list - 16 20 Bytes