Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CONSERVED HYPOTHETICAL PROTEIN PFU-178653-001 FROM PYROCOCCUS FURIOSUS
 
Authors :  J. Habel, W. Zhou, J. Chang, M. Zhao, H. Xu, L. Chen, D. Lee, D. Nguyen, S. - P. Horanyi, Q. Florence, W. Tempel, D. Lin, H. Zhang, J. Praissman, F. E Jr. , M. W. W. Adams, Z. -J. Liu, J. P. Rose, B. -C. Wang, Southeast Colla For Structural Genomics (Secsg)
Date :  19 Dec 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, Psi, Conserved Hypothetical Protein, Pyrococcus Furiosus, Hyperthermophile, Secsg, The Southeast Collaboratory For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Habel, W. Zhou, J. Chang, M. Zhao, H. Xu, L. Chen, D. Lee, D. Nguyen, S. -H. Chang, P. Horanyi, Q. Florence, W. Tempel, D. Lin, H. Zhang, J. Praissman, F. E. Jenney Jr. , M. W. W. Adams, Z. -J. Liu, J. P. Rose, B. -C. Wang
Conserved Hypothetical Protein Pfu-178653-001 From Pyrococcus Furiosus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2UNX1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , GLU A:99 , HOH A:209 , HOH A:240BINDING SITE FOR RESIDUE UNX A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YB3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:63 -Pro A:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YB3)

(-) Exons   (0, 0)

(no "Exon" information available for 1YB3)

(-) 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:166
 aligned with Q8U4C0_PYRFU | Q8U4C0 from UniProtKB/TrEMBL  Length:167

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
         Q8U4C0_PYRFU     2 MLKEVHELLNRIWGDIFELREELKEELKGFTVEEVSEVFNAYLYIDGKWEEMKYPHPAFAVKPGGEVGATPQGFYFVFAFPKEELSKEFIEDVIRAFEKLFIYGAENFLEDFYNFEHPISGDEVWDRIVNSDEEMINFEVDLGFDKEEVKREIKRFIELARRYNLL 167
               SCOP domains d1yb3a1 A:2-167 Hypothetical protein PF0168                                                                                                                            SCOP domains
               CATH domains -1yb3A00 A:3-167 Bira Bifunctional Protein; Domain 2                                                                                                                   CATH domains
               Pfam domains ------DUF3201-1yb3A01 A:8-157                                                                                                                               ---------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...eee...eeee..eeee....eeeeeee..eeeeee..eeeeeeeee.hhhhhhhhhhhhhhh.eeeee.......eeee.....hhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb3 A   2 mLKEVHELLNRIWGDIFELREELKEELKGFTVEEVSEVFNAYLYIDGKWEEmKYPHPAFAVKPGGEVGATPQGFYFVFAFPKEELSKEFIEDVIRAFEKLFIYGAENFLEDFYNFEHPISGDEVWDRIVNSDEEmINFEVDLGFDKEEVKREIKRFIELARRYNLL 167
                            |       11        21        31        41        51 |      61        71        81        91       101       111       121       131    |  141       151       161      
                            |                                                 53-MSE                                                                            136-MSE                           
                            2-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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3201] (1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1YB3)

 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 ]
    UNX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:63 - Pro A:64   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1yb3
    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
  Q8U4C0_PYRFU | Q8U4C0
    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
  Q8U4C0_PYRFU | Q8U4C0
    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 1YB3)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YB3)