Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  CRYSTAL STRUCTURE OF PROJECT PH0463 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  K. Shimizu, N. Kunishima, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  02 Dec 04  (Deposition) - 29 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Shimizu, N. Kunishima
Crystal Structure Of Project Id Ph0463 From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH0463
    Chains: A, B, C
    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: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (1x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1ADN3Ligand/IonADENOSINE
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 42)
No.NameCountTypeFull Name
1ADN6Ligand/IonADENOSINE
2MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 21)
No.NameCountTypeFull Name
1ADN3Ligand/IonADENOSINE
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , HIS A:41 , ASP A:68 , PRO A:69 , VAL A:71 , THR A:125 , PHE B:181 , ASN B:183 , TYR B:212 , VAL B:234 , ASN B:235 , MSE B:236BINDING SITE FOR RESIDUE ADN A 500
2AC2SOFTWAREASP B:7 , PHE B:8 , HIS B:41 , ILE B:67 , ASP B:68 , PRO B:69 , THR B:125 , PHE C:181 , ASN C:183 , TYR C:212 , VAL C:234 , MSE C:236BINDING SITE FOR RESIDUE ADN B 501
3AC3SOFTWAREPHE A:181 , ASN A:183 , TYR A:212 , VAL A:234 , ASN A:235 , MSE A:236 , HIS C:41 , ASP C:68 , PRO C:69 , VAL C:71 , THR C:125BINDING SITE FOR RESIDUE ADN C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WU8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WU8)

(-) Exons   (0, 0)

(no "Exon" information available for 1WU8)

(-) 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:256
 aligned with O58212_PYRHO | O58212 from UniProtKB/TrEMBL  Length:256

    Alignment length:256
                                    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      
         O58212_PYRHO     1 MITLTTDFGLKGPYVGEMKVAMLRINPNAKIVDVTHSVTRHSILEGSFVMEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEMLALPGSHDYLEIAVNMGSAAERLNVKVGDELRVRLL 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh....eeeee..........eeeeee..eeeee....hhhhhh...eeeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhh.eeeehhhhh.......eee..eeeeeeeee.....eeeeee......eeee....eeee...hhhhh....eeee.....eeeeee...hhhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu8 A   1 mITLTTDFGLKGPYVGEmKVAmLRINPNAKIVDVTHSVTRHSILEGSFVmEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEmLALPGSHDYLEIAVNmGSAAERLNVKVGDELRVRLL 256
                            |       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      
                            |               18-MSE                          50-MSE                                                                                                                                                                   220-MSE         236-MSE                
                            1-MSE               22-MSE                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with O58212_PYRHO | O58212 from UniProtKB/TrEMBL  Length:256

    Alignment length:256
                                    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      
         O58212_PYRHO     1 MITLTTDFGLKGPYVGEMKVAMLRINPNAKIVDVTHSVTRHSILEGSFVMEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEMLALPGSHDYLEIAVNMGSAAERLNVKVGDELRVRLL 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh....eeeee..........eeeeee..eeeee....hhhhhh...eeeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhh.eee.hhhhh.......eee..eeeeeeeee.....eee.........eeee....eeee...hhhhh....eeee......eeeee...hhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu8 B   1 mITLTTDFGLKGPYVGEmKVAmLRINPNAKIVDVTHSVTRHSILEGSFVmEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEmLALPGSHDYLEIAVNmGSAAERLNVKVGDELRVRLL 256
                            |       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      
                            1-MSE           18-MSE                          50-MSE                                                                                                                                                                   220-MSE         236-MSE                
                                                22-MSE                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:256
 aligned with O58212_PYRHO | O58212 from UniProtKB/TrEMBL  Length:256

    Alignment length:256
                                    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      
         O58212_PYRHO     1 MITLTTDFGLKGPYVGEMKVAMLRINPNAKIVDVTHSVTRHSILEGSFVMEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEMLALPGSHDYLEIAVNMGSAAERLNVKVGDELRVRLL 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SAM_adeno_trans-1wu8C01 C:1-253                                                                                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) SAM_adeno_trans-1wu8C02 C:1-253                                                                                                                                                                                                                              --- Pfam domains (2)
           Pfam domains (3) SAM_adeno_trans-1wu8C03 C:1-253                                                                                                                                                                                                                              --- Pfam domains (3)
         Sec.struct. author .eeeee......hhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh....eeeee..........eeeeee..eeeee....hhhhhh...eeeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhh.eee.hhhhh.......eee..eeeeeeeee.....eee.........eeee.hhheeee...hhhhh....eeee......eeeee...hhhhhhh.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wu8 C   1 mITLTTDFGLKGPYVGEmKVAmLRINPNAKIVDVTHSVTRHSILEGSFVmEQVVKYSPKGTVHVGVIDPGVGTERRAIVIEGDQYLVVPDNGLATLPLKHIKVKSVYEIIPDKIRKFTGWEISSTFHGRDIFGPAGALIEKGIHPEEFGREIPVDSIVKLNVEPRKEGDVWILKVIYIDDFGNVILNLENYEKPRTVELLDFNLRLPYLETYGLVEKGEmLALPGSHDYLEIAVNmGSAAERLNVKVGDELRVRLL 256
                            |       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      
                            1-MSE           18-MSE                          50-MSE                                                                                                                                                                   220-MSE         236-MSE                
                                                22-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  (0, 0)

(no "SCOP Domain" information available for 1WU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WU8)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: SAM_adeno_trans] (4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1WU8)

 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
    ADN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wu8)
 
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
  1wu8
    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
  O58212_PYRHO | O58212
    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
  O58212_PYRHO | O58212
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O58212_PYRHO | O58212: 2wr8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WU8)