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

(-) Description

Title :  CRYSTAL STRUCTURE OF LACTAM UTILIZATION PROTEIN FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Dec 03  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tim-Barrel, Lactam Utilization Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of Lactam Utilization Protein From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0271 PROTEIN PH0986
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODON PLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: LACTAM UTILIZATION PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1V6T)

(-) Sites  (0, 0)

(no "Site" information available for 1V6T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V6T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V6T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V6T)

(-) Exons   (0, 0)

(no "Exon" information available for 1V6T)

(-) 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:249
 aligned with Y986_PYRHO | O58714 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
           Y986_PYRHO     1 MRVDLNSDLGESFGRYKLGLDEEVMKYITSANVACGWHAGDPLVMRKTVRLAKENDVQVGAHPGYPDLMGFGRRYMKLTPEEARNYILYQVGALYAFAKAEGLELQHVKPHGALYNAMVKEEDLARAVIEGILDFDKDLILVTLSNSRVADIAEEMGLKVAHEVFADRAYNPDGTLVPRGRPGAVIEDKEEIAERVISMVKDGGIRAINGEWVDLKVDTICVHGDNPKAVEITSYIRKVLEEEGVKIVPMKEFI 254
               SCOP domains d1v6ta_ A: Hypothetical protein PH0986                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -LamB_YcsF-1v6tA01 A:2-243                                                                                                                                                                                                                         ----------- Pfam domains
         Sec.struct. author .eeeeeeee..........hhhhhh....eeeee......hhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh..eeeee...eee.....eee-----ee..hhhhhhhhhhhhhhhheee.....eee....eee....hhhhhhhhhhhhhhhhhh..ee.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v6t A   1 MRVDLNSDLGESFGRYKLGLDEEVMKYITSANVACGWHAGDPLVMRKTVRLAKENDVQVGAHPGYPDLMGFGRRYMKLTPEEARNYILYQVGALYAFAKAEGLELQHVKPHGALYNAMVKEEDLARAVIEGILDFDKDLILVTLSNSRVADIAEEMGLKVAHEVFADRAYNPDGTLVP-----AVIEDKEEIAERVISMVKDGGIRAINGEWVDLKVDTICVHGDNPKAVEITSYIRKVLEEEGVKIVPMKEFI 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -   |   190       200       210       220       230       240       250    
                                                                                                                                                                                                           178   184
   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)

(no "CATH Domain" information available for 1V6T)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GH_CE (28)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Y986_PYRHO | O58714)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

 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 1v6t)
 
  Sites
(no "Sites" information available for 1v6t)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v6t)
 
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
  1v6t
    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
  Y986_PYRHO | O58714
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  Y986_PYRHO | O58714
    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 1V6T)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V6T)