Header list of 1eki.pdb file
Complete list - 29 20 Bytes
HEADER DNA 08-MAR-00 1EKI
TITLE AVERAGE SOLUTION STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND
TITLE 2 COBALT
CAVEAT 1EKI DA A 8 HAS WRONG CHIRALITY AT ATOM C3' DA B 18 HAS WRONG
CAVEAT 2 1EKI CHIRALITY AT ATOM C3' CPH A 33 HAS WRONG CHIRALITY AT ATOM
CAVEAT 3 1EKI C1'
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*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 CHROMOMYCIN A3 (1GL-2GL-DXB-
COMPND 6 DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DRUG BOUND IN THE MINOR GROOVE OF DNA, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.GOCHIN
REVDAT 5 29-JUL-20 1EKI 1 CAVEAT COMPND REMARK HETNAM
REVDAT 5 2 1 LINK SITE ATOM
REVDAT 4 28-DEC-11 1EKI 1 CAVEAT VERSN
REVDAT 3 24-FEB-09 1EKI 1 VERSN
REVDAT 2 23-MAY-00 1EKI 1 JRNL
REVDAT 1 20-MAR-00 1EKI 0
JRNL AUTH M.GOCHIN
JRNL TITL A HIGH-RESOLUTION STRUCTURE OF A DNA-CHROMOMYCIN-CO(II)
JRNL TITL 2 COMPLEX DETERMINED FROM PSEUDOCONTACT SHIFTS IN NUCLEAR
JRNL TITL 3 MAGNETIC RESONANCE.
JRNL REF STRUCTURE FOLD.DES. V. 8 441 2000
JRNL REFN ISSN 0969-2126
JRNL PMID 10801486
JRNL DOI 10.1016/S0969-2126(00)00124-6
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH K.TU,M.GOCHIN
REMARK 1 TITL STRUCTURE DETERMINATION BY RESTRAINED MOLECULAR DYNAMICS
REMARK 1 TITL 2 USING NMR PSEUDOCONTACT SHIFTS AS EXPERIMENTALLY DETERMINED
REMARK 1 TITL 3 CONSTRAINTS
REMARK 1 REF J.AM.CHEM.SOC. V. 121 9276 1999
REMARK 1 REFN ISSN 0002-7863
REMARK 1 DOI 10.1021/JA9904540
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 1.7, X-PLOR 3.0, 3.851
REMARK 3 AUTHORS : DELAGLIO AND BAX (NMRPIPE), BRUNGER (MODIFIED
REMARK 3 GOCHIN AND TU) (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS, ISOLATED SPIN-PAIR
REMARK 3 APPROXIMATION FOR NOE'S; PSEUDOCONTACT SHIFT REFINEMENT
REMARK 4
REMARK 4 1EKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-00.
REMARK 100 THE DEPOSITION ID IS D_1000010675.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6
REMARK 210 IONIC STRENGTH : 110MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 2MM DNA-DRUG COMPLEX, 25 DEGREES
REMARK 210 C, IN BUFFER (100MM NACL, 10MM
REMARK 210 NA BORATE), FINAL PH 6.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 13C-1H HMQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : OMEGA
REMARK 210 SPECTROMETER MANUFACTURER : GE
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SPARKY 3.0, FELIX 2.1
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGE STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES AS WELL AS 2D 13C-1H HETERONUCLEAR
REMARK 210 CORRELATION
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, C, D, E, F
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 O1 2GL D 1 C6 CPH B 23 1.41
REMARK 500 O1 2GL C 1 C6 CPH A 33 1.42
REMARK 500 O1 DDA E 1 C2 CPH B 23 1.42
REMARK 500 O1 DDA F 1 C2 CPH A 33 1.45
REMARK 500 O2 DC A 6 H21 DG B 13 1.59
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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -9.9 DEGREES
REMARK 500 DG A 3 C3' - O3' - P ANGL. DEV. = 17.6 DEGREES
REMARK 500 DG A 4 P - O5' - C5' ANGL. DEV. = 18.1 DEGREES
REMARK 500 DG A 4 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES
REMARK 500 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DA A 7 P - O5' - C5' ANGL. DEV. = 11.0 DEGREES
REMARK 500 DA A 7 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES
REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG B 13 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES
REMARK 500 DG B 13 C4' - C3' - C2' ANGL. DEV. = -9.8 DEGREES
REMARK 500 DG B 13 C3' - O3' - P ANGL. DEV. = 17.3 DEGREES
REMARK 500 DG B 14 P - O5' - C5' ANGL. DEV. = 17.6 DEGREES
REMARK 500 DG B 14 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DG B 14 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES
REMARK 500 DC B 15 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES
REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DA B 17 C3' - O3' - P ANGL. DEV. = 16.1 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 2 0.10 SIDE CHAIN
REMARK 500 DA A 7 0.08 SIDE CHAIN
REMARK 500 DT B 12 0.10 SIDE CHAIN
REMARK 500 DG B 14 0.06 SIDE CHAIN
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 CPH A 33
REMARK 610 CPH B 23
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 CO A 41 CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CPH A 33 O9
REMARK 620 2 CPH A 33 O1 102.5
REMARK 620 3 CPH A 33 C9 35.6 83.5
REMARK 620 4 CPH A 33 C1 85.3 22.9 61.2
REMARK 620 5 CPH B 23 O9 120.4 115.3 155.1 138.1
REMARK 620 6 CPH B 23 O1 127.9 88.0 97.9 86.6 98.9
REMARK 620 7 CPH B 23 C9 151.5 90.9 172.6 112.8 32.3 77.0
REMARK 620 8 CPH B 23 C1 146.1 91.8 118.8 98.1 78.7 20.9 56.3
REMARK 620 N 1 2 3 4 5 6 7
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1EKH RELATED DB: PDB
REMARK 900 FAMILY OF 6 STRUCTURES
REMARK 900 RELATED ID: 1D83 RELATED DB: PDB
DBREF 1EKI A 1 8 PDB 1EKI 1EKI 1 8
DBREF 1EKI B 11 18 PDB 1EKI 1EKI 11 18
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 2GL C 1 25
HET 1GL C 2 23
HET 2GL D 1 25
HET 1GL D 2 23
HET DDA E 1 20
HET DDA E 2 19
HET ERI E 3 28
HET DDA F 1 20
HET DDA F 2 19
HET ERI F 3 28
HET CO A 41 1
HET CPH A 33 49
HET CPH B 23 49
HETNAM 2GL 4-O-ACETYL-2,6-DIDEOXY-BETA-D-GALACTOPYRANOSE
HETNAM 1GL 2,6-DIDEOXY-4-O-METHYL-ALPHA-D-GALACTOPYRANOSE
HETNAM DDA BETA-D-OLIVOPYRANOSE
HETNAM ERI 3-C-METHYL-4-O-ACETYL-ALPHA-L-OLIVOPYRANOSE
HETNAM CO COBALT (II) ION
HETNAM CPH (1S)-5-DEOXY-1-O-METHYL-1-C-[(2R,3S)-3,5,7,10-
HETNAM 2 CPH TETRAHYDROXY-6-METHYL-4-OXO-1,2,3,4-
HETNAM 3 CPH TETRAHYDROANTHRACEN-2-YL]-D-XYLULOSE
HETSYN DDA 2,6-DIDEOXY-BETA-D-MANNOSE
HETSYN CPH NONE
FORMUL 3 2GL 2(C8 H14 O5)
FORMUL 3 1GL 2(C7 H14 O4)
FORMUL 5 DDA 4(C6 H12 O4)
FORMUL 5 ERI 2(C9 H16 O5)
FORMUL 7 CO CO 2+
FORMUL 8 CPH 2(C21 H24 O9)
LINK O3 2GL C 1 C1 1GL C 2 1555 1555 1.46
LINK O3 2GL D 1 C1 1GL D 2 1555 1555 1.45
LINK O3 DDA E 1 C1 DDA E 2 1555 1555 1.42
LINK O3 DDA E 2 C1 ERI E 3 1555 1555 1.43
LINK O3 DDA F 1 C1 DDA F 2 1555 1555 1.43
LINK O3 DDA F 2 C1 ERI F 3 1555 1555 1.44
LINK O9 CPH A 33 CO CO A 41 1555 1555 1.90
LINK O1 CPH A 33 CO CO A 41 1555 1555 1.93
LINK C9 CPH A 33 CO CO A 41 1555 1555 2.41
LINK C1 CPH A 33 CO CO A 41 1555 1555 2.75
LINK CO CO A 41 O9 CPH B 23 1555 1555 1.91
LINK CO CO A 41 O1 CPH B 23 1555 1555 1.86
LINK CO CO A 41 C9 CPH B 23 1555 1555 2.57
LINK CO CO A 41 C1 CPH B 23 1555 1555 2.77
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
Complete list - 29 20 Bytes