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

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE PUTATIVE N-TYPE ATP PYROPHOSPHATASE FROM PYROCOCCUS FURIOSUS, THE NORTHEAST STRUCTURAL GENOMICS TARGET PFR23
 
Authors :  F. Forouhar, I. Lee, R. Xiao, T. B. Acton, G. T. Montelione, J. Hunt, L. To Northeast Structural Genomics Consortium (Nesg)
Date :  16 Apr 11  (Deposition) - 11 May 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, Alpha-Beta Protein, N-Type Atp Pyrophosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, N. Saadat, M. Hussain, J. Seetharaman, I. Lee, H. Janjua, R. Xiao, R. Shastry, T. B. Acton, G. T. Montelione, L. Tong
A Large Conformational Change In The Putative Atp Pyrophosphatase Pf0828 Induced By Atp Binding.
Acta Crystallogr. , Sect. F V. 67 1323 2011
PubMed-ID: 22102225  |  Reference-DOI: 10.1107/S1744309111031447

(-) Compounds

Molecule 1 - N-TYPE ATP PYROPHOSPHATASE SUPERFAMILY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PF0828
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3RJZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RJZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RJZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RJZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RJZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3RJZ)

(-) 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:210
 aligned with Q8U2K6_PYRFU | Q8U2K6 from UniProtKB/TrEMBL  Length:229

    Alignment length:229
                                                                                                                                                                                                                                                            229  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      |  
         Q8U2K6_PYRFU     3 GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYHTINANLTDLQARALGIPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGALASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESK--   -
               SCOP domains d3rjza_ A: Putative N-type ATP pyropho        sphatase PF0828                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --ATP_bind_4-3rjzA01 A:5-226                                                                                                                                                                                                    ----- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeeeeeee.--------....hhhhhhhhhhh..eeeeee------hhhhhhhhhh.....eee..---..hhhhhhhhhhhhh..eee......hhhhhhhhhhhh..eeeeeeee....hhhhh....hhhhhhhhhhhhhhhh.........eeeeeee.....eeeeeeeeeee--....eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rjz A   3 GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTmVSE--------TINANLTDLQARALGIPLVKGFT------EVEDLKRVLSGLKIQGIVAG---SKYQRKRIEKVAKELGLEVYTPAWGRDAKEYmRELLNLGFKImVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDmPLFKYKIVVDKAKKV--PCTSSGKLIIEEAHLESKLE 231
                                    12        22        32    |  | -      | 52        62        |-     |  82        92    |  102       112       122       132       142|      152       162       172       182       192 |     202      |212       222         
                                                             37-MSE      49                    71     78                 97 101                            132-MSE    143-MSE                                            194-MSE        209  |                   
                                                                                                                                                                                                                                           212
   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  (0, 0 ; only for superseded entry 1RU8: 2,4)

(no "CATH Domain" information available for 3RJZ, only for superseded entry 1RU8 replaced by 3RJZ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8U2K6_PYRFU | Q8U2K6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3rjz)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rjz)
 
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
  3rjz
    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
  Q8U2K6_PYRFU | Q8U2K6
    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)
  (no 'Enzyme Classificator' available)
    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
  Q8U2K6_PYRFU | Q8U2K6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8U2K6_PYRFU | Q8U2K6: 3rk0 3rk1

(-) Related Entries Specified in the PDB File

3rk0 THIS IS THE AMP-BOUND STRUCTURE
3rk1 THIS IS THE ATP-BOUND STRUCTURE