Header list of 1amd.pdb file
Complete list - 16 202 Bytes
HEADER DNA 12-JUN-97 1AMD
TITLE NMR STUDY OF DNA (5'-D(*TP*GP*TP*AP*CP*A)-3') SELF-COMPLEMENTARY
TITLE 2 DUPLEX COMPLEXED WITH A BIS-DAUNORUBICIN WP-652, MINIMIZED AVERAGE
TITLE 3 STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*TP*AP*CP*A)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: WP652 IS AN INTERCALATOR
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS COMPLEX (DEOXYRIBONUCLEIC ACID-DRUG), BIS-INTERCALATOR, DAUNORUBICIN,
KEYWDS 2 DNA, DEOXYRIBONUCLEIC ACID
EXPDTA SOLUTION NMR
AUTHOR H.ROBINSON,A.H.-J.WANG
REVDAT 4 16-FEB-22 1AMD 1 REMARK
REVDAT 3 24-FEB-09 1AMD 1 VERSN
REVDAT 2 01-APR-03 1AMD 1 JRNL
REVDAT 1 17-SEP-97 1AMD 0
JRNL AUTH H.ROBINSON,W.PRIEBE,J.B.CHAIRES,A.H.WANG
JRNL TITL BINDING OF TWO NOVEL BISDAUNORUBICINS TO DNA STUDIED BY NMR
JRNL TITL 2 SPECTROSCOPY.
JRNL REF BIOCHEMISTRY V. 36 8663 1997
JRNL REFN ISSN 0006-2960
JRNL PMID 9289011
JRNL DOI 10.1021/BI970842J
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: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE.
REMARK 4
REMARK 4 1AMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170995.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 288
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 : 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA 750
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 : 1
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: IONIC_STRENGTH: 20 MM PRESSURE: NULL SOLVENT SYSTEM: H2O
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 DC A 5 C5 DC A 5 C6 0.052
REMARK 500 DT B 7 C5' DT B 7 C4' 0.115
REMARK 500 DT B 7 C5 DT B 7 C7 0.051
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 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG A 2 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES
REMARK 500 DG A 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -11.4 DEGREES
REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DT A 3 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 DA B 10 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC B 11 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DA B 12 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES
REMARK 500 DA B 12 O4' - C1' - N9 ANGL. DEV. = 5.7 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 1 0.08 SIDE CHAIN
REMARK 500 DT B 7 0.09 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 BNR B 13
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AL9 RELATED DB: PDB
REMARK 900 MINIMIZED AVERAGE STRUCTURE
DBREF 1AMD A 1 6 PDB 1AMD 1AMD 1 6
DBREF 1AMD B 7 12 PDB 1AMD 1AMD 7 12
SEQRES 1 A 6 DT DG DT DA DC DA
SEQRES 1 B 6 DT DG DT DA DC DA
HET BNR B 13 150
HETNAM BNR BIS-DAUNORUBICIN
HETSYN BNR WP652
FORMUL 3 BNR C62 H66 N2 O20 2+
SITE 1 AC1 8 DT A 1 DG A 2 DT A 3 DA A 4
SITE 2 AC1 8 DT B 9 DA B 10 DC B 11 DA B 12
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 - 16 202 Bytes