Header list of 1vyx.pdb file
Complete list - y 2 2 Bytes
HEADER ZINC-BINDING PROTEIN 07-MAY-04 1VYX
TITLE SOLUTION STRUCTURE OF THE KSHV K3 N-TERMINAL DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ORF K3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RING FINGER, RESIDUES 1-60;
COMPND 5 SYNONYM: K3RING;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 8;
SOURCE 3 ORGANISM_COMMON: KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS;
SOURCE 4 ORGANISM_TAXID: 37296;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA
KEYWDS ZINC-BINDING PROTEIN, RING DOMAIN, CROSS-BRACE MOTIF
EXPDTA SOLUTION NMR
NUMMDL 28
AUTHOR R.B.DODD,M.D.ALLEN,S.E.BROWN,C.M.SANDERSON,L.M.DUNCAN,P.J.LEHNER,
AUTHOR 2 M.BYCROFT,R.J.READ
REVDAT 7 02-MAY-18 1VYX 1 REMARK
REVDAT 6 24-JAN-18 1VYX 1 SOURCE
REVDAT 5 24-FEB-09 1VYX 1 VERSN
REVDAT 4 03-MAY-05 1VYX 1 ATOM
REVDAT 3 19-JAN-05 1VYX 1 REVDAT
REVDAT 2 15-DEC-04 1VYX 1 JRNL
REVDAT 1 01-OCT-04 1VYX 0
JRNL AUTH R.B.DODD,M.D.ALLEN,S.E.BROWN,C.M.SANDERSON,L.M.DUNCAN,
JRNL AUTH 2 P.J.LEHNER,M.BYCROFT,R.J.READ
JRNL TITL SOLUTION STRUCTURE OF THE KAPOSI'S SARCOMA-ASSOCIATED
JRNL TITL 2 HERPESVIRUS K3 N-TERMINAL DOMAIN REVEALS A NOVEL E2-BINDING
JRNL TITL 3 C4HC3-TYPE RING DOMAIN
JRNL REF J.BIOL.CHEM. V. 279 53840 2004
JRNL REFN ISSN 0021-9258
JRNL PMID 15465811
JRNL DOI 10.1074/JBC.M409662200
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 1VYX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-04.
REMARK 100 THE DEPOSITION ID IS D_1290020025.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298.0
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 100.0
REMARK 210 PRESSURE : AMBIENT ATM
REMARK 210 SAMPLE CONTENTS : 50 MM POTASSIUM PHOSPHATE (PH
REMARK 210 6.0), CONTAINING 50 MM NACL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; DQF-COSY; HNCACB;
REMARK 210 CBCACONH; HNCO; HNCACO; 13C-HSQC;
REMARK 210 HNHB
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWIN-NMR, ANSIG, XPLOR3.8
REMARK 210 METHOD USED : XPLOR3.8
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 30
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 28
REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS GREATER THAN
REMARK 210 0.25A, NO ANGLE VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDAR TRIPLE-
REMARK 210 RESONANCE METHODS ON 13C-15N-LABELLED K3-RING DOMAIN
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 H CYS A 50 O VAL A 55 1.57
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 GLU A 4 -175.90 -49.68
REMARK 500 1 ASP A 5 153.54 70.28
REMARK 500 1 ASN A 18 39.21 169.99
REMARK 500 1 GLU A 19 106.45 -59.31
REMARK 500 1 ARG A 20 96.15 -62.26
REMARK 500 1 CYS A 24 166.70 172.77
REMARK 500 1 CYS A 26 -161.68 -76.19
REMARK 500 1 ARG A 46 64.19 68.94
REMARK 500 1 ASN A 58 72.63 49.47
REMARK 500 2 GLU A 2 -145.18 35.25
REMARK 500 2 ASP A 3 -74.42 -95.29
REMARK 500 2 ASN A 18 73.49 145.82
REMARK 500 2 ARG A 20 96.49 -61.56
REMARK 500 2 CYS A 26 -158.99 36.79
REMARK 500 3 ASP A 3 -163.52 -100.56
REMARK 500 3 ASP A 5 -175.13 52.45
REMARK 500 3 ASN A 18 55.16 119.12
REMARK 500 3 ARG A 20 98.47 -61.62
REMARK 500 3 ALA A 23 -32.16 -139.13
REMARK 500 3 CYS A 26 -101.76 -62.59
REMARK 500 3 ARG A 46 75.91 57.10
REMARK 500 3 ASN A 58 82.13 40.59
REMARK 500 4 ASP A 3 -151.03 -142.25
REMARK 500 4 GLU A 4 -101.94 -115.37
REMARK 500 4 ASP A 5 160.96 60.57
REMARK 500 4 ASN A 18 39.89 167.78
REMARK 500 4 GLU A 19 106.48 -59.07
REMARK 500 4 ARG A 20 95.76 -62.55
REMARK 500 4 CYS A 24 166.74 173.05
REMARK 500 4 CYS A 26 -162.12 -79.60
REMARK 500 4 ARG A 46 68.21 69.64
REMARK 500 4 ASN A 58 92.24 43.94
REMARK 500 5 GLU A 4 -40.60 -157.35
REMARK 500 5 ASP A 5 81.63 -69.31
REMARK 500 5 ASN A 13 60.97 64.23
REMARK 500 5 ASN A 18 32.69 -168.71
REMARK 500 5 ARG A 20 95.20 -66.61
REMARK 500 5 CYS A 24 167.86 171.79
REMARK 500 5 CYS A 26 -158.06 40.06
REMARK 500 5 ARG A 46 63.25 61.59
REMARK 500 6 GLU A 2 -76.77 -145.21
REMARK 500 6 ASP A 5 111.53 56.19
REMARK 500 6 ASN A 18 44.65 167.00
REMARK 500 6 GLU A 19 105.37 -59.10
REMARK 500 6 ARG A 20 95.56 -62.09
REMARK 500 6 CYS A 24 166.68 176.42
REMARK 500 6 CYS A 26 -168.49 -76.20
REMARK 500 6 ARG A 46 73.86 39.79
REMARK 500 6 THR A 48 -26.15 74.38
REMARK 500 7 ASP A 3 -168.33 49.44
REMARK 500
REMARK 500 THIS ENTRY HAS 237 RAMACHANDRAN OUTLIERS.
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 ARG A 20 0.31 SIDE CHAIN
REMARK 500 1 ARG A 22 0.22 SIDE CHAIN
REMARK 500 1 ARG A 35 0.29 SIDE CHAIN
REMARK 500 1 ARG A 46 0.32 SIDE CHAIN
REMARK 500 1 ARG A 60 0.29 SIDE CHAIN
REMARK 500 2 ARG A 20 0.24 SIDE CHAIN
REMARK 500 2 ARG A 22 0.28 SIDE CHAIN
REMARK 500 2 ARG A 35 0.30 SIDE CHAIN
REMARK 500 2 ARG A 46 0.10 SIDE CHAIN
REMARK 500 2 ARG A 60 0.28 SIDE CHAIN
REMARK 500 3 ARG A 20 0.32 SIDE CHAIN
REMARK 500 3 ARG A 22 0.28 SIDE CHAIN
REMARK 500 3 ARG A 35 0.14 SIDE CHAIN
REMARK 500 3 ARG A 46 0.32 SIDE CHAIN
REMARK 500 3 ARG A 60 0.10 SIDE CHAIN
REMARK 500 4 ARG A 20 0.31 SIDE CHAIN
REMARK 500 4 ARG A 22 0.26 SIDE CHAIN
REMARK 500 4 ARG A 35 0.27 SIDE CHAIN
REMARK 500 4 ARG A 46 0.32 SIDE CHAIN
REMARK 500 4 ARG A 60 0.26 SIDE CHAIN
REMARK 500 5 ARG A 20 0.24 SIDE CHAIN
REMARK 500 5 ARG A 22 0.29 SIDE CHAIN
REMARK 500 5 ARG A 35 0.22 SIDE CHAIN
REMARK 500 5 ARG A 46 0.19 SIDE CHAIN
REMARK 500 6 ARG A 20 0.27 SIDE CHAIN
REMARK 500 6 ARG A 22 0.20 SIDE CHAIN
REMARK 500 6 ARG A 35 0.25 SIDE CHAIN
REMARK 500 6 ARG A 46 0.27 SIDE CHAIN
REMARK 500 6 ARG A 60 0.28 SIDE CHAIN
REMARK 500 7 ARG A 20 0.27 SIDE CHAIN
REMARK 500 7 ARG A 22 0.20 SIDE CHAIN
REMARK 500 7 ARG A 35 0.22 SIDE CHAIN
REMARK 500 7 ARG A 46 0.31 SIDE CHAIN
REMARK 500 7 ARG A 60 0.26 SIDE CHAIN
REMARK 500 8 ARG A 20 0.23 SIDE CHAIN
REMARK 500 8 ARG A 22 0.26 SIDE CHAIN
REMARK 500 8 ARG A 35 0.13 SIDE CHAIN
REMARK 500 8 ARG A 46 0.20 SIDE CHAIN
REMARK 500 8 ARG A 60 0.31 SIDE CHAIN
REMARK 500 9 ARG A 20 0.15 SIDE CHAIN
REMARK 500 9 ARG A 22 0.22 SIDE CHAIN
REMARK 500 9 ARG A 35 0.29 SIDE CHAIN
REMARK 500 9 ARG A 46 0.32 SIDE CHAIN
REMARK 500 9 ARG A 60 0.32 SIDE CHAIN
REMARK 500 10 ARG A 20 0.30 SIDE CHAIN
REMARK 500 10 ARG A 22 0.30 SIDE CHAIN
REMARK 500 10 ARG A 35 0.08 SIDE CHAIN
REMARK 500 10 ARG A 46 0.31 SIDE CHAIN
REMARK 500 10 ARG A 60 0.30 SIDE CHAIN
REMARK 500 11 ARG A 20 0.30 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 136 PLANE DEVIATIONS.
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 A1061 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 37 SG
REMARK 620 2 CYS A 12 SG 119.1
REMARK 620 3 CYS A 9 SG 95.2 102.1
REMARK 620 4 HIS A 34 ND1 132.9 100.6 100.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1062 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 24 SG
REMARK 620 2 CYS A 50 SG 106.6
REMARK 620 3 CYS A 26 SG 104.6 122.3
REMARK 620 4 CYS A 53 SG 100.9 106.1 114.0
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1061
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1062
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CHC RELATED DB: PDB
REMARK 900 EQUINE HERPES VIRUS-1 (C3HC4, OR RING DOMAIN) (NMR, 1 STRUCTURE)
DBREF 1VYX A 1 60 UNP P90495 P90495 1 60
SEQRES 1 A 60 MET GLU ASP GLU ASP VAL PRO VAL CYS TRP ILE CYS ASN
SEQRES 2 A 60 GLU GLU LEU GLY ASN GLU ARG PHE ARG ALA CYS GLY CYS
SEQRES 3 A 60 THR GLY GLU LEU GLU ASN VAL HIS ARG SER CYS LEU SER
SEQRES 4 A 60 THR TRP LEU THR ILE SER ARG ASN THR ALA CYS GLN ILE
SEQRES 5 A 60 CYS GLY VAL VAL TYR ASN THR ARG
HET ZN A1061 1
HET ZN A1062 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLY A 28 ASN A 32 5 5
HELIX 2 2 HIS A 34 ARG A 46 1 13
SHEET 1 AA 2 VAL A 8 CYS A 9 0
SHEET 2 AA 2 GLU A 14 GLU A 15 -1 O GLU A 14 N CYS A 9
LINK ZN ZN A1061 SG CYS A 37 1555 1555 2.28
LINK ZN ZN A1061 SG CYS A 12 1555 1555 2.33
LINK ZN ZN A1061 SG CYS A 9 1555 1555 2.41
LINK ZN ZN A1061 ND1 HIS A 34 1555 1555 2.20
LINK ZN ZN A1062 SG CYS A 24 1555 1555 2.20
LINK ZN ZN A1062 SG CYS A 50 1555 1555 2.28
LINK ZN ZN A1062 SG CYS A 26 1555 1555 2.27
LINK ZN ZN A1062 SG CYS A 53 1555 1555 2.35
SITE 1 AC1 4 CYS A 9 CYS A 12 HIS A 34 CYS A 37
SITE 1 AC2 4 CYS A 24 CYS A 26 CYS A 50 CYS A 53
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 - y 2 2 Bytes