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(-) Description

Title :  CRYSTAL STRUCTURE OF THE JCV LARGE T-ANTIGEN ORIGIN BINDING DOMAIN
 
Authors :  G. Meinke, A. Bohm, P. Bullock
Date :  23 Oct 13  (Deposition) - 05 Mar 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Origin Binding Domain, Dna Replication, Binds Dna, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Meinke, P. J. Phelan, R. Kalekar, J. Shin, J. Archambault, A. Bohm, P. A. Bullock
Insights Into The Initiation Of Jc Virus Dna Replication Derived From The Crystal Structure Of The T-Antigen Origin Binding Domain.
Plos Pathog. V. 10 03966 2014
PubMed-ID: 24586168  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003966

(-) Compounds

Molecule 1 - LARGE T ANTIGEN
    Chains: A
    EC Number: 3.6.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: ORIGIN BINDING DOMAIN
    Gene: LARGE T ANTIGEN
    Organism Common: JCPYV
    Organism Scientific: JC POLYOMAVIRUS
    Organism Taxid: 10632
    Synonym: LT, LT-AG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:167 , LYS A:168 , LEU A:216 , CYS A:217 , THR A:218 , PHE A:219 , SER A:220 , HOH A:591BINDING SITE FOR RESIDUE TLA A 301
2AC2SOFTWAREHIS A:202 , ARG A:203 , HIS A:204 , ALA A:208 , HOH A:409 , HOH A:418 , HOH A:437 , HOH A:487BINDING SITE FOR RESIDUE TLA A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NBP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:240 -Pro A:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NBP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NBP)

(-) Exons   (0, 0)

(no "Exon" information available for 4NBP)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains d4nbpa_ A: The origin DNA-binding domain of SV40 T-antigen                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeeehhhhhhhhhhh......eeeee..hhhhhhhhh.....eeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbp A 133 VEDPKDFPVDLHAFLSQAVFSNRTVASFAVYTTKEKAQILYKKLMEKYSVTFISRHGFGGHNILFFLTPHRHRVSAINNYCQKLCTFSFLICKGVNKEYLFYSALCRQPYAVVEESIQGGLKEHDFNPE 261
                                   142       152       162       172       182       192       202       212       222       232       242       252
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NBP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NBP)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  4nbp
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LT_POVJC | P03072: 4lif 4lmd 5cyn 5j40 5j47 5j4v 5j4y

(-) Related Entries Specified in the PDB File

4lif JCV OBD
4lmd JCV OBD