Header list of 1bj6.pdb file
Complete list - 16 20 Bytes
HEADER VIRAL PROTEIN/DNA 03-JUL-98 1BJ6
TITLE 1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*AP*CP*GP*CP*C)-3');
COMPND 3 CHAIN: D;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: NUCLEOCAPSID PROTEIN 7;
COMPND 7 CHAIN: A;
COMPND 8 FRAGMENT: RESIDUES 12-53;
COMPND 9 SYNONYM: (12-53)NCP7;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 5 ORGANISM_TAXID: 11676;
SOURCE 6 STRAIN: MAL
KEYWDS COMPLEX (NUCLEOCAPSID PROTEIN-DNA), NUCLEIC ACID, RETROVIRUS, VIRUS
KEYWDS 2 MORPHOGENESIS, ZINC FINGER, VIRAL PROTEIN-DNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR H.DEMENE,N.MORELLET,V.TEILLEUX,T.HUYNH-DINH,H.DE ROCQUIGNY,
AUTHOR 2 M.C.FOURNIE-ZALUSKI,B.P.ROQUES
REVDAT 5 16-FEB-22 1BJ6 1 REMARK LINK
REVDAT 4 24-FEB-09 1BJ6 1 VERSN
REVDAT 3 01-APR-03 1BJ6 1 JRNL
REVDAT 2 23-MAR-99 1BJ6 3 COMPND REMARK TITLE DBREF
REVDAT 2 2 3 HEADER ATOM SOURCE SEQRES
REVDAT 2 3 3 JRNL KEYWDS
REVDAT 1 02-FEB-99 1BJ6 0
JRNL AUTH N.MORELLET,H.DEMENE,V.TEILLEUX,T.HUYNH-DINH,H.DE ROCQUIGNY,
JRNL AUTH 2 M.C.FOURNIE-ZALUSKI,B.P.ROQUES
JRNL TITL STRUCTURE OF THE COMPLEX BETWEEN THE HIV-1 NUCLEOCAPSID
JRNL TITL 2 PROTEIN NCP7 AND THE SINGLE-STRANDED PENTANUCLEOTIDE
JRNL TITL 3 D(ACGCC).
JRNL REF J.MOL.BIOL. V. 283 419 1998
JRNL REFN ISSN 0022-2836
JRNL PMID 9769215
JRNL DOI 10.1006/JMBI.1998.2098
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DISCOVER
REMARK 3 AUTHORS : BIOSYM
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE PROTEIN PART OF THE STRUCTURE WAS
REMARK 3 FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING
REMARK 3 CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION
REMARK 3 WAS DOCKED APPROXIMATIVELY TO THE PROTEIN BASED ON THE 28
REMARK 3 INTERMOLECULAR NOES. THE DOCKED STRUCTURE WAS ENERGY-MINIMIZED
REMARK 3 UNDER NOES RESTRAINTS. THIS INITIAL COMPLEXED STRUCTURE WAS THEN
REMARK 3 USED FOR A SECOND SET OF SIMULATED ANNEALING CALCULATION.
REMARK 4
REMARK 4 1BJ6 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_1000171818.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : LOW SALT CONDITIONS
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : WATER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX600
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : BRUKER DISNMR DISNMR, BIOSYM/MSI
REMARK 210 METHOD USED : DYNAMICAL SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION AND
REMARK 210 LOWEST TOTAL ENERGY
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A
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 D 2 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DA D 1 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 2 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 3 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 3 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 4 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DC D 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 4 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 5 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 6 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 6 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 6 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 7 DA D 1 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES
REMARK 500 7 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 7 DC D 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 7 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 7 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 8 DA D 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 8 DC D 2 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 8 DC D 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 8 DC D 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 9 DA D 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 9 DC D 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 9 DC D 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 10 DA D 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES
REMARK 500 10 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 10 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ASN A 17 -85.72 -143.86
REMARK 500 1 THR A 50 28.65 -161.23
REMARK 500 2 CYS A 15 117.55 -33.96
REMARK 500 2 ASN A 17 -88.64 -82.29
REMARK 500 2 THR A 50 40.68 -172.92
REMARK 500 2 GLU A 51 -81.19 -14.51
REMARK 500 3 LYS A 14 67.84 -163.23
REMARK 500 3 CYS A 15 111.70 -0.79
REMARK 500 3 ASN A 17 -64.58 -155.66
REMARK 500 3 HIS A 44 -161.19 -160.04
REMARK 500 3 THR A 50 37.32 -179.33
REMARK 500 3 GLU A 51 -78.97 -17.62
REMARK 500 3 ARG A 52 40.55 29.50
REMARK 500 4 ASN A 17 -77.67 -75.05
REMARK 500 4 LYS A 38 -76.43 -56.19
REMARK 500 4 THR A 50 29.80 -165.18
REMARK 500 4 ARG A 52 67.85 25.12
REMARK 500 5 VAL A 13 -57.21 -139.07
REMARK 500 5 LYS A 14 105.20 76.92
REMARK 500 5 PHE A 16 48.99 -79.62
REMARK 500 5 ASN A 17 -74.27 -151.54
REMARK 500 5 LYS A 38 -71.83 -56.15
REMARK 500 5 HIS A 44 -160.84 -103.60
REMARK 500 5 THR A 50 36.22 -177.15
REMARK 500 5 GLU A 51 -76.29 -22.36
REMARK 500 5 ARG A 52 74.27 56.40
REMARK 500 6 CYS A 15 121.74 -28.88
REMARK 500 6 PHE A 16 49.25 -83.92
REMARK 500 6 ASN A 17 -77.47 -152.33
REMARK 500 6 HIS A 44 -148.58 -97.03
REMARK 500 6 THR A 50 38.04 -160.90
REMARK 500 6 ARG A 52 -152.65 -66.60
REMARK 500 7 PHE A 16 39.21 -91.44
REMARK 500 7 ASN A 17 -75.41 -148.06
REMARK 500 7 THR A 50 25.47 -152.14
REMARK 500 7 GLU A 51 -120.10 -91.45
REMARK 500 7 ARG A 52 134.69 156.21
REMARK 500 8 ASN A 17 -80.14 -149.44
REMARK 500 8 THR A 50 36.70 -177.99
REMARK 500 8 GLU A 51 -80.12 -7.06
REMARK 500 9 CYS A 15 124.00 -34.95
REMARK 500 9 ASN A 17 -83.80 -154.88
REMARK 500 9 THR A 50 19.07 -141.97
REMARK 500 9 ARG A 52 85.87 -163.77
REMARK 500 10 CYS A 15 114.95 -21.44
REMARK 500 10 ASN A 17 -73.79 -151.95
REMARK 500 10 LYS A 38 -74.14 -57.14
REMARK 500 10 HIS A 44 -162.78 -116.76
REMARK 500 10 ARG A 52 79.12 -169.22
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 DG D 3 0.06 SIDE CHAIN
REMARK 500 5 DC D 2 0.09 SIDE CHAIN
REMARK 500 8 DC D 2 0.09 SIDE CHAIN
REMARK 500 9 DC D 5 0.07 SIDE CHAIN
REMARK 500 10 ARG A 52 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
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 ZN A 54H ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 15 SG
REMARK 620 2 CYS A 18 SG 114.9
REMARK 620 3 HIS A 23 NE2 105.4 109.4
REMARK 620 4 CYS A 28 SG 109.9 107.9 109.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 55H ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 36 SG
REMARK 620 2 CYS A 39 SG 113.9
REMARK 620 3 HIS A 44 NE2 106.0 108.0
REMARK 620 4 CYS A 49 SG 106.8 112.4 109.4
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ZNB
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: ZINC-BINDING SITES.
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 54H
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 55H
DBREF 1BJ6 A 13 53 UNP Q74084 Q74084_9HIV1 390 430
DBREF 1BJ6 D 1 5 PDB 1BJ6 1BJ6 1 5
SEQRES 1 D 5 DA DC DG DC DC
SEQRES 1 A 42 ASN VAL LYS CYS PHE ASN CYS GLY LYS GLU GLY HIS THR
SEQRES 2 A 42 ALA ARG ASN CYS ARG ALA PRO ARG LYS LYS GLY CYS TRP
SEQRES 3 A 42 LYS CYS GLY LYS GLU GLY HIS GLN MET LYS ASP CYS THR
SEQRES 4 A 42 GLU ARG GLN
HET ZN A 54H 1
HET ZN A 55H 1
HETNAM ZN ZINC ION
FORMUL 3 ZN 2(ZN 2+)
LINK SG CYS A 15 ZN ZN A 54H 1555 1555 2.31
LINK SG CYS A 18 ZN ZN A 54H 1555 1555 2.26
LINK NE2 HIS A 23 ZN ZN A 54H 1555 1555 2.04
LINK SG CYS A 28 ZN ZN A 54H 1555 1555 2.23
LINK SG CYS A 36 ZN ZN A 55H 1555 1555 2.30
LINK SG CYS A 39 ZN ZN A 55H 1555 1555 2.27
LINK NE2 HIS A 44 ZN ZN A 55H 1555 1555 2.03
LINK SG CYS A 49 ZN ZN A 55H 1555 1555 2.27
SITE 1 ZNB 7 CYS A 15 CYS A 18 HIS A 23 CYS A 28
SITE 2 ZNB 7 CYS A 36 CYS A 39 HIS A 44
SITE 1 AC1 4 CYS A 15 CYS A 18 HIS A 23 CYS A 28
SITE 1 AC2 4 CYS A 36 CYS A 39 HIS A 44 CYS A 49
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