Header list of 1kvh.pdb file
Complete list - 23 20 Bytes
HEADER DNA 26-JAN-02 1KVH
TITLE NCSI-GB-BULGE-DNA COMPLEX INDUCED FORMATION OF A DNA BULGE STRUCTURE
TITLE 2 BY A MOLECULAR WEDGE LIGAND-POST-ACTIVATED NEOCARZINOSTATIN
TITLE 3 CHROMOPHORE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*CP*GP*AP*TP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*CP*AP*AP*TP*TP*CP*GP*GP*G)-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS DNA
EXPDTA SOLUTION NMR
NUMMDL 7
AUTHOR X.GAO,A.STASSINOPOULOS,J.JI,Y.KWON,S.BARE,I.H.GOLDBERG
REVDAT 3 23-FEB-22 1KVH 1 REMARK
REVDAT 2 24-FEB-09 1KVH 1 VERSN
REVDAT 1 19-JUN-02 1KVH 0
JRNL AUTH X.GAO,A.STASSINOPOULOS,J.JI,Y.KWON,S.BARE,I.H.GOLDBERG
JRNL TITL INDUCED FORMATION OF A DNA BULGE STRUCTURE BY A MOLECULAR
JRNL TITL 2 WEDGE LIGAND-POSTACTIVATED NEOCARZINOSTATIN CHROMOPHORE.
JRNL REF BIOCHEMISTRY V. 41 5131 2002
JRNL REFN ISSN 0006-2960
JRNL PMID 11955061
JRNL DOI 10.1021/BI012112O
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.01
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 A TOTAL OF 681 NMR RESTRAINTS IS USED TO DERIVE THE FINAL REFINED
REMARK 3 STRUCTURES.
REMARK 3 THE TOTAL RESTRAINTS CONSIST OF 590 OF NOE-DERIVED DISTANCE
REMARK 3 RESTRAINTS AND 91 OF DIHEDRAL ANGLE RESTRAINTS.
REMARK 3 ESPECIALLY, 85 OF INTERMOLECULAR DISTANCE RESTRAINTS ARE DERIVED
REMARK 3 WHICH REPRESENT THE INTERACTION BETWEEN THE DRUG AND THE BULGE
REMARK 3 DUPLEX.
REMARK 4
REMARK 4 1KVH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-02.
REMARK 100 THE DEPOSITION ID IS D_1000015382.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 270; 278
REMARK 210 PH : 6.4; 6.4
REMARK 210 IONIC STRENGTH : 0.1M NACL, 10 MM SODIUM
REMARK 210 PHOSPHATE; 0.1M NACL, 10 MM
REMARK 210 SODIUM PHOSPHATE
REMARK 210 PRESSURE : NULL; NULL
REMARK 210 SAMPLE CONTENTS : CA. 1 MM NCSI-GB-BULGE-DNA
REMARK 210 COMPLEX; 0.1 M NACL, 10 MM
REMARK 210 SODIUM PHOSPHATE, AND 0.1 MM
REMARK 210 EDTA BUFFER (PH 6.4); 90% H2O,
REMARK 210 10% D2O; CA. 1 MM NCSI-GB-BULGE-
REMARK 210 DNA COMPLEX; 0.1 M NACL, 10 MM
REMARK 210 SODIUM PHOSPHATE, AND 0.1 MM
REMARK 210 EDTA BUFFER (PH 6.4); 99.96% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; PE-COSY;
REMARK 210 TOCSY, H-P COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : DISTANCE GEOMETRY (DG),
REMARK 210 RESTRAINED MOLECULAR DYNAMICS
REMARK 210 (RMDS), AND RELAXATION MATRIX
REMARK 210 REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 7
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND
REMARK 210 HETERONUCLEAR TECHNIQUES
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 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' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DG B 9 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DA B 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DA B 11 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 1 DA B 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA B 12 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DA B 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 16 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DG B 17 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 1 DG B 17 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 17 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG B 18 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG B 18 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG A 7 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 DG B 9 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DG B 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG B 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 246 ANGLE DEVIATIONS.
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 1 DT B 14 0.07 SIDE CHAIN
REMARK 500 2 DT B 14 0.07 SIDE CHAIN
REMARK 500 3 DT B 14 0.07 SIDE CHAIN
REMARK 500 4 DT B 14 0.07 SIDE CHAIN
REMARK 500 5 DT B 14 0.07 SIDE CHAIN
REMARK 500 6 DT B 14 0.07 SIDE CHAIN
REMARK 500 7 DA A 5 0.08 SIDE CHAIN
REMARK 500 7 DT B 14 0.11 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 NCS B 21
DBREF 1KVH A 1 8 PDB 1KVH 1KVH 1 8
DBREF 1KVH B 9 18 PDB 1KVH 1KVH 9 18
SEQRES 1 A 8 DC DC DC DG DA DT DG DC
SEQRES 1 B 10 DG DC DA DA DT DT DC DG DG DG
HET NCS B 21 84
HETNAM NCS SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,
HETNAM 2 NCS 1'-[5-HYDROXY-9-[2-METHYLAMINO-2,6-
HETNAM 3 NCS DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-
HETNAM 4 NCS YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-
HETNAM 5 NCS INDACEN-2-ONE]]
FORMUL 3 NCS C35 H36 N O12 1+
SITE 1 AC1 8 DC A 3 DG A 4 DA A 5 DT A 6
SITE 2 AC1 8 DA B 11 DA B 12 DT B 13 DT 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 - 23 20 Bytes