Header list of 1dsc.pdb file
Complete list - 25 201 Bytes
HEADER DNA/ANTIBIOTIC 10-AUG-96 1DSC
TITLE NMR STUDY OF DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3') SELF-COMPLEMENTARY
TITLE 2 DUPLEX COMPLEXED WITH ACTINOMYCIN D, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: ACTINOMYCIN D;
COMPND 7 CHAIN: C;
COMPND 8 SYNONYM: DACTINOMYCIN
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: STREPTOMYCES ANTIBIOTICUS;
SOURCE 5 ORGANISM_TAXID: 1890
KEYWDS ACTINOMYCIN D, DACTINOMYCIN, ANTIBIOTIC, ANTI CANCER, ANTITUMOR,
KEYWDS 2 CHROMOPHORE, DEPSIPEPTIDE, DNA-ANTIBIOTIC COMPLEX
EXPDTA SOLUTION NMR
AUTHOR C.LIAN,H.ROBINSON,A.H.-J.WANG
REVDAT 4 27-JUL-11 1DSC 1 ATOM REMARK
REVDAT 3 13-JUL-11 1DSC 1 VERSN
REVDAT 2 24-FEB-09 1DSC 1 VERSN
REVDAT 1 07-DEC-96 1DSC 0
JRNL AUTH C.LIAN,H.ROBINSON,A.H.-J.WANG
JRNL TITL STRUCTURE OF ACTINOMYCIN D BOUND WITH (GAAGCTTC)2 AND
JRNL TITL 2 (GATGCTTC)2 AND ITS BINDING TO THE (CAG)N:(CTG)N TRIPLET
JRNL TITL 3 SEQUENCE BY NMR ANALYSIS
JRNL REF J.AM.CHEM.SOC. V. 118 8791 1996
JRNL REFN ISSN 0002-7863
JRNL DOI 10.1021/JA961631P
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: NULL
REMARK 4
REMARK 4 1DSC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : VXR 500
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR, SPEDREF
REMARK 210 METHOD USED : NOE-RMD
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NULL
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 400
REMARK 400 COMPOUND
REMARK 400 ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE
REMARK 400 ACTINOMYCIN FAMILY.
REMARK 400 HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: ACTINOMYCIN D
REMARK 400 CHAIN: C
REMARK 400 COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11
REMARK 400 DESCRIPTION: ACTINOMYCIN D CONSISTS OF TWO PENTAMER
REMARK 400 RINGS LINKED BY THE CHROMOPHORE (PXZ)
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 DG A 1 C5' DG A 1 C4' 0.046
REMARK 500 DT A 6 C5 DT A 6 C7 0.039
REMARK 500 DG B 9 C5' DG B 9 C4' 0.048
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. = 3.4 DEGREES
REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES
REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG A 4 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES
REMARK 500 DG A 4 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES
REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 8.4 DEGREES
REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES
REMARK 500 DT A 6 C5' - C4' - O4' ANGL. DEV. = 9.2 DEGREES
REMARK 500 DT A 6 O4' - C1' - C2' ANGL. DEV. = -8.2 DEGREES
REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 8.7 DEGREES
REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES
REMARK 500 DA B 11 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 DA B 11 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES
REMARK 500 DA B 11 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES
REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.3 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 DC A 8 0.08 SIDE CHAIN
REMARK 500 DC B 16 0.08 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 CHAIN C OF ACTINOMYCIN D
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1A7Z RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN Z3
REMARK 900 RELATED ID: 209D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH
REMARK 900 D(GAAGCTTC)2
REMARK 900 RELATED ID: 1UNM RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH
REMARK 900 NON-COMPLEMENTARY DNA
REMARK 900 RELATED ID: 1I3W RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (CGATCGATCG)2
REMARK 900 RELATED ID: 1A7Y RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D
REMARK 900 RELATED ID: 1FJA RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (AAGCGCTT)2
REMARK 900 RELATED ID: 173D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (GAAGCTTC)2
REMARK 900 RELATED ID: 2D55 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (GAAGCTTC)2
REMARK 900 RELATED ID: 1L1V RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH
REMARK 900 MISMATCHED DNA (GTCACCGAC)
REMARK 900 RELATED ID: 316D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (GAAGCTTC)2
REMARK 900 RELATED ID: 1DSD RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (GATGCTTC)2
REMARK 900 RELATED ID: 1MNV RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (ATGCTGCAT)2
REMARK 900 RELATED ID: 1UNJ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A
REMARK 900 NON-COMPLEMENTARY DNA (TTAGT)2
REMARK 900 RELATED ID: 1OVF RELATED DB: PDB
REMARK 900 SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA
REMARK 900 (CCGTTTTGTGG)2
REMARK 900 RELATED ID: 1QFI RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ACTINOMYCIN X2
DBREF 1DSC A 1 8 PDB 1DSC 1DSC 1 8
DBREF 1DSC B 9 16 PDB 1DSC 1DSC 9 16
DBREF 1DSC C 1 11 NOR NOR00228 NOR00228 1 11
SEQRES 1 A 8 DG DA DA DG DC DT DT DC
SEQRES 1 B 8 DG DA DA DG DC DT DT DC
SEQRES 1 C 11 THR DVA PRO SAR MVA PXZ THR DVA PRO SAR MVA
HET DVA C 2 16
HET SAR C 4 10
HET MVA C 5 19
HET PXZ C 6 32
HET DVA C 8 16
HET SAR C 10 10
HET MVA C 11 19
HETNAM DVA D-VALINE
HETNAM SAR SARCOSINE
HETNAM MVA N-METHYLVALINE
HETNAM PXZ 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-
HETNAM 2 PXZ PHENOXAZIN-3-ONE
HETSYN PXZ PHENOXAZINE
FORMUL 3 DVA 2(C5 H11 N O2)
FORMUL 3 SAR 2(C3 H7 N O2)
FORMUL 3 MVA 2(C6 H13 N O2)
FORMUL 3 PXZ C16 H12 N2 O4
LINK C THR C 1 N DVA C 2 1555 1555 1.30
LINK OG1 THR C 1 C MVA C 5 1555 1555 1.33
LINK N THR C 1 C PXZ C 6 1555 1555 1.31
LINK C DVA C 2 N PRO C 3 1555 1555 1.31
LINK C PRO C 3 N SAR C 4 1555 1555 1.30
LINK C SAR C 4 N MVA C 5 1555 1555 1.32
LINK C' PXZ C 6 N THR C 7 1555 1555 1.30
LINK C THR C 7 N DVA C 8 1555 1555 1.30
LINK OG1 THR C 7 C MVA C 11 1555 1555 1.31
LINK C DVA C 8 N PRO C 9 1555 1555 1.30
LINK C PRO C 9 N SAR C 10 1555 1555 1.31
LINK C SAR C 10 N MVA C 11 1555 1555 1.32
CISPEP 1 DVA C 2 PRO C 3 0 28.91
CISPEP 2 PRO C 3 SAR C 4 0 -0.76
CISPEP 3 DVA C 8 PRO C 9 0 19.63
CISPEP 4 PRO C 9 SAR C 10 0 0.46
SITE 1 AC1 9 DA A 3 DG A 4 DC A 5 DT A 6
SITE 2 AC1 9 DT A 7 DA B 11 DG B 12 DC B 13
SITE 3 AC1 9 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
Complete list - 25 201 Bytes