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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYDROGENASE ASSEMBLY CHAPERONE HYPC/HUPF FAMILY PROTEIN FROM SHEWANELLA ONEIDENSIS MR-1
 
Authors :  Y. Kim, T. Skarina, O. Onopriyenko, A. M. Edwards, A. Savchenko, A. Joac Midwest Center For Structural Genomics (Mcsg)
Date :  12 May 08  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Small Beta-Barrel, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, T. Skarina, O. Onopriyenko, A. M. Edwards, A. Savchenko, A. Joachimiak
Crystal Structure Of The Hydrogenase Assembly Chaperone Hypc/Hupf Family Protein From Shewanella Oneidensis Mr-1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROGENASE ASSEMBLY CHAPERONE HYPC/HUPF
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP11
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    GeneHYPC, SO_2092
    Organism ScientificSHEWANELLA ONEIDENSIS
    Organism Taxid211586
    StrainMR-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3D3R)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:2 -B:2

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D3R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D3R)

(-) Exons   (0, 0)

(no "Exon" information available for 3D3R)

(-) 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:83
 aligned with Q8EF93_SHEON | Q8EF93 from UniProtKB/TrEMBL  Length:81

    Alignment length:83
                                   1                                                                           
                                   | 3        13        23        33        43        53        63        73   
          Q8EF93_SHEON    - -------MCLSIPSQVVAVDNERQSVTVDTLGVRRDVSSHLMTEPLAIGDYVLIHIGFVMNKIDRNDALQSLELYQEIVSKLE 76
               SCOP domains -------d3d3ra1 A:1-76 Hydrogenase expression/formation protein HypC                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..ee...eeeeeee....eeeeee..eeeeee............eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  3d3r A -6 ENLYFQGmCLSIPSQVVAVDNERQSVTVDTLGVRRDVSSHLmTEPLAIGDYVLIHIGFVmNKIDRNDALQSLELYQEIVSKLE 76
                                   | 3        13        23        33 |      43        53        63        73   
                                   1-MSE                            35-MSE            53-MSE                   

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with Q8EF93_SHEON | Q8EF93 from UniProtKB/TrEMBL  Length:81

    Alignment length:80
                                1                                                                           
                                |    6        16        26        36        46        56        66        76
          Q8EF93_SHEON    - ----MCLSIPSQVVAVDNERQSVTVDTLGVRRDVSSHLMTEPLAIGDYVLIHIGFVMNKIDRNDALQSLELYQEIVSKLE 76
               SCOP domains d3d3rb_ B: Hydrogenase expression/formation protein HypC                         SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....eeeeeee....eeeeee..eeeeee.hhh........eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  3d3r B -3 YFQGmCLSIPSQVVAVDNERQSVTVDTLGVRRDVSSHLmTEPLAIGDYVLIHIGFVmNKIDRNDALQSLELYQEIVSKLE 76
                                |    6        16        26        36        46      | 56        66        76
                                1-MSE                            35-MSE            53-MSE                   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D3R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D3R)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3D3R)

 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 3d3r)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3d3r)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3d3r
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8EF93_SHEON | Q8EF93
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q8EF93_SHEON | Q8EF93
    Protein Disorder PredictionDisEMBL | 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 3D3R)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3D3R)