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

(-) Description

Title :  CRYSTAL STRUCTURE OF HYDROGENASE MATURATION FACTOR HYPB FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  K. B. Wong, T. Li
Date :  08 Sep 09  (Deposition) - 22 Sep 10  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Chan, T. Li, C. Wong, K. B. Wong
Structural Basis For Gtp-Dependent Dimerization Of Hydrogenase Maturation Factor Hypb.
Plos One V. 7 30547 2012
PubMed-ID: 22276211  |  Reference-DOI: 10.1371/JOURNAL.PONE.0030547

(-) Compounds

Molecule 1 - HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPB)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:91 , CYS A:92 , HIS A:93 , GLU B:91 , CYS B:92 , HIS B:93BINDING SITE FOR RESIDUE CL A1214

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:122
2B:92 -B:122

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WSM)

(-) Sequences/Alignments

Asymmetric/Biological 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:203
 aligned with O28903_ARCFU | O28903 from UniProtKB/TrEMBL  Length:221

    Alignment length:203
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
         O28903_ARCFU    11 LAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIGNEVKIGAMLGDVVSKADYERVRRFGIKAEAISTGKECHLDAHMIYHRLKKFSDCDLLLIENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWIDFLRGILN 213
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhh.....eeeee....hhhhhhhhhh...eeee.........hhhhhhhhhhhhh...eeeee.....hhhhhh.....eeeeeeehhh..hhhhhhhhhhhh..eeeeehhhhh.....hhhhhhhhhhhhh...eeee........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsm A  11 LAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIGNEVKIGAMLGDVVSKADYERVRRFGIKAEAISTGKECHLDAHMIYHRLKKFSDCDLLLIENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWIDFLRGILN 213
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with O28903_ARCFU | O28903 from UniProtKB/TrEMBL  Length:221

    Alignment length:203
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208   
         O28903_ARCFU     9 DLLAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIGNEVKIGAMLGDVVSKADYERVRRFGIKAEAISTGKECHLDAHMIYHRLKKFSDCDLLLIENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWIDFLRGI 211
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------cobW-2wsmB01 B:31-192                                                                                                                                             ------------------- Pfam domains (1)
           Pfam domains (2) ----------------------cobW-2wsmB02 B:31-192                                                                                                                                             ------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhh.......eeeee..----------------eee.........hhhhhhhhhhhhh...eeeee.....hhhhhh.....eeeeeeehhh..hhhhhhhhhhh...eeeee.hhhh.....hhhhhhhhhhhhh...eeeee.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsm B   9 DLLAENKRLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERIGNEVKIGAMLGD----------------AEAISTGKECHLDAHMIYHRLKKFSDCDLLLIENVGNLICPVDFDLGENYRVVMVSVTEGDDVVEKHPEIFRVADLIVINKVALAEAVGADVEKMKADAKLINPRAKIIEMDLKTGKGFEEWIDFLRGI 211
                                    18        28        38        48        58       | -         -    |   88        98       108       118       128       138       148       158       168       178       188       198       208   
                                                                                    66               83
   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  (0, 0)

(no "SCOP Domain" information available for 2WSM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WSM)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O28903_ARCFU | O28903)
molecular function
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
biological process
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wsm)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2wsm
    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
  O28903_ARCFU | O28903
    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
  O28903_ARCFU | O28903
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2WSM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WSM)