Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARGINASE FROM THERMUS THERMOPHILUS
 
Authors :  T. S. Kumarevel, P. Karthe, S. Kuramitsu, S. Yokoyama, Riken Structur Genomics/Proteomics Initiative (Rsgi)
Date :  20 Feb 07  (Deposition) - 14 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Arginase, Ttha1496, Thermus Thermophilus, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, P. Karthe, S. Kuramitsu, S. Yokoyama
Crystal Structure Of The Arginase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARGINASE
    Chains: A
    EC Number: 3.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TTHH1496
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2EF4)

(-) Sites  (0, 0)

(no "Site" information available for 2EF4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EF4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EF4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EF4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EF4)

(-) Exons   (0, 0)

(no "Exon" information available for 2EF4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:282
 aligned with Q5SI78_THET8 | Q5SI78 from UniProtKB/TrEMBL  Length:291

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
         Q5SI78_THET8     2 ERVAVVGVPMDLGANRRGVDMGPSALRYARLLEQLEDLGYTVEDLGDVPVSLARASRRRGRGLAYLEEIRAAALVLKERLAALPEGVFPIVLGGDHSLSMGSVAGAARGRRVGVVWVDAHADFNTPETSPSGNVHGMPLAVLSGLGHPRLTEVFRAVDPKDVVLVGVRSLDPGEKRLLKEAGVRVYTMHEVDRLGVARIAEEVLKHLQGLPLHVSLDADVLDPTLAPGVGTPVPGGLTYREAHLLMEILAESGRVQSLDLVEVNPILDERNRTAEMLVGLALSLLGKRIF 291
               SCOP domains d2ef4a_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ef4A00 A:2-291  [code=3.40.800.10, no name defined]                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.......--------..hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhh.....eeeee...............hhhhhhhhhhh...hhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh....eeeeee.hhh................hhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ef4 A   2 ERVAVVGVPMDLGANRRGVDMGPSALRYARLLEQLEDLGYTVEDLGDVPVSLAR--------LAYLEEIRAAALVLKERLAALPEGVFPIVLGGDHSLSMGSVAGAARGRRVGVVWVDAHADFNTPETSPSGNVHGMPLAVLSGLGHPRLTEVFRAVDPKDVVLVGVRSLDPGEKRLLKEAGVRVYTMHEVDRLGVARIAEEVLKHLQGLPLHVSLDADVLDPTLAPGVGTPVPGGLTYREAHLLMEILAESGRVQSLDLVEVNPILDERNRTAEMLVGLALSLLGKRIF 291
                                    11        21        31        41        51   |     -  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
                                                                                55       64
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EF4)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SI78_THET8 | Q5SI78)
molecular function
    GO:0004053    arginase activity    Catalysis of the reaction: L-arginine + H2O = L-ornithine + urea.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2ef4)
 
  Sites
(no "Sites" information available for 2ef4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ef4)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ef4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q5SI78_THET8 | Q5SI78
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.3.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q5SI78_THET8 | Q5SI78
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SI78_THET8 | Q5SI78: 2ef5 2eiv

(-) Related Entries Specified in the PDB File

2ef5 RELATED ID: TTK003000367.3 RELATED DB: TARGETDB