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

(-) Description

Title :  A HYPOTHETICAL PROTEIN PH1897 FROM PYROCOCCUS HORIKOSHII WITH SIMILARITIES FOR INOSITOL-1 MONOPHOSPHATASE
 
Authors :  E. Inagaki, T. H. Tahirov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Mar 04  (Deposition) - 06 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Inagaki, T. H. Tahirov
The Crystal Structure Of Hypothetical Protein Ph1897 From Pyrococcus Horikoshii With Similarities For Inositol-1-Monophosphatase.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1897
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:5 , TRP B:6 , ARG B:7 , TYR B:113 , HOH B:1076 , HOH B:1081 , HOH B:1225BINDING SITE FOR RESIDUE EDO B 1001
2AC2SOFTWAREASP A:87 , ALA A:174 , ILE A:175 , HOH A:1030 , HOH A:1035 , HOH A:1082 , HOH A:1113BINDING SITE FOR RESIDUE EDO A 1002
3AC3SOFTWAREGLY A:157 , LYS A:158 , GLY A:159 , GLY B:157 , LYS B:158 , THR B:160BINDING SITE FOR RESIDUE EDO A 1003
4AC4SOFTWAREASP B:218 , LEU B:219 , VAL B:234 , ASN B:235 , HOH B:1127BINDING SITE FOR RESIDUE EDO B 1004
5AC5SOFTWAREVAL B:82 , SER B:102 , THR B:200 , ASP B:201 , ALA B:203 , ALA B:204 , HOH B:1010 , HOH B:1114BINDING SITE FOR RESIDUE EDO B 1005
6AC6SOFTWARELYS B:8 , ASP B:74 , GLY B:76 , SER B:77BINDING SITE FOR RESIDUE EDO B 1006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VDW)

(-) 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:248
 aligned with O59523_PYRHO | O59523 from UniProtKB/TrEMBL  Length:254

    Alignment length:253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
         O59523_PYRHO     2 SVKTWRKIAIDIIRDFDHNIMPLFGNPKASETISISPSGDETKVVDKVAENIIISKFKDLGVNVVSEEIGRIDQGSDYTVVVDPLDGSYNFINGIPFFAVSVAIFHEKDPIYAFIYEPIVERLYEGIPGKGSYLNGEKIKVRELAEKPSISFYTKGKGTKIIDKVKRTRTLGAIALELAYLARGALDAVVDIRNYLRPTDIAAGVVIAREAGAIVKDLDGKDVEITFSATEKVNIIAANNEELLETILRSIEK 254
               SCOP domains d1vdwa_ A: Archaeal inositol monoph     osphatase/fructose-1,6-bisphosphatase                                                                                                                                                                                 SCOP domains
               CATH domains 1vdwA01 A:2-140 Fructose-1,6-Bispho     sphatase, subunit A, domain 1                                                                      1vdwA02 A:141-254  [code=3.40.190.80, no name defined]                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eee.-----.eehhhhhhhhhhhhhhhhh..eeee...eee.....eeeeeeeeehhhhhhh.....eeeeeeee..eeeeeeeeehhhheeeeee...eeee..eee.........eeeee....hhhhhhh..eee...hhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhhhhh..eee................eeeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdw A   2 SVKTWRKIAIDIIRDFDHNIMPLFGNPKASETISI-----ETKVVDKVAENIIISKFKDLGVNVVSEEIGRIDQGSDYTVVVDPLDGSYNFINGIPFFAVSVAIFHEKDPIYAFIYEPIVERLYEGIPGKGSYLNGEKIKVRELAEKPSISFYTKGKGTKIIDKVKRTRTLGAIALELAYLARGALDAVVDIRNYLRPTDIAAGVVIAREAGAIVKDLDGKDVEITFSATEKVNIIAANNEELLETILRSIEK 254
                                    11        21        31    |    -|       51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
                                                             36    42                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with O59523_PYRHO | O59523 from UniProtKB/TrEMBL  Length:254

    Alignment length:253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
         O59523_PYRHO     2 SVKTWRKIAIDIIRDFDHNIMPLFGNPKASETISISPSGDETKVVDKVAENIIISKFKDLGVNVVSEEIGRIDQGSDYTVVVDPLDGSYNFINGIPFFAVSVAIFHEKDPIYAFIYEPIVERLYEGIPGKGSYLNGEKIKVRELAEKPSISFYTKGKGTKIIDKVKRTRTLGAIALELAYLARGALDAVVDIRNYLRPTDIAAGVVIAREAGAIVKDLDGKDVEITFSATEKVNIIAANNEELLETILRSIEK 254
               SCOP domains d1vdwb_ B: Archaeal inositol monop     hosphatase/fructose-1,6-bisphosphatase                                                                                                                                                                                 SCOP domains
               CATH domains 1vdwB01 B:2-140 Fructose-1,6-Bisph     osphatase, subunit A, domain 1                                                                      1vdwB02 B:141-254  [code=3.40.190.80, no name defined]                                                             CATH domains
           Pfam domains (1) Inositol_P-1vdwB01 B:2-254                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Inositol_P-1vdwB02 B:2-254                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh.hhhhhheee-----..eehhhhhhhhhhhhhhhhh..eeee...eee.....eeeeeeeeehhhhhhh.....eeeeeeee..eeeeeeeeehhhheeeeee...eeee..eee.........eeeee....hhhhhh...eee...hhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhhhhh..eee................eeeeee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdw B   2 SVKTWRKIAIDIIRDFDHNIMPLFGNPKASETIS-----DETKVVDKVAENIIISKFKDLGVNVVSEEIGRIDQGSDYTVVVDPLDGSYNFINGIPFFAVSVAIFHEKDPIYAFIYEPIVERLYEGIPGKGSYLNGEKIKVRELAEKPSISFYTKGKGTKIIDKVKRTRTLGAIALELAYLARGALDAVVDIRNYLRPTDIAAGVVIAREAGAIVKDLDGKDVEITFSATEKVNIIAANNEELLETILRSIEK 254
                                    11        21        31   |    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
                                                            35    41
   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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Phospoesterase (42)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O59523_PYRHO | O59523)
biological process
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vdw)
 

(-) 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
  1vdw
    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
  O59523_PYRHO | O59523
    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
  O59523_PYRHO | O59523
    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 1VDW)

(-) Related Entries Specified in the PDB File

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