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

(-) Description

Title :  CRYSTAL STRUCTURE OF A GLUCOSE-6-PHOSPHATE ISOMERASE LIKE PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  A. Yoshihiro, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yoshihiro, S. Yokoyama, S. Kuramitsu
Crystal Structure Of A Glucose-6-Phosphate Isomerase Like Protein From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WIW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:37 -Pro A:38
2Gly B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WIW)

(-) 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:282
 aligned with Q5SIM3_THET8 | Q5SIM3 from UniProtKB/TrEMBL  Length:290

    Alignment length:284
                                    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       260       270       280    
         Q5SIM3_THET8     1 MRDLDREETYLVDRTGLALELRDLVGTGPVPGEAYPGPHAALGYGEGQFAALLSGLPDWGEEGTLFLLEGGYDLGEAAGMALLAETGRARVVRVGFRPGVEVHIPPSPLAPYRYLRFLLLATGREEVLRSVDEALLEERRRLGPEVPVEENPAKFLAYTLLERLPLFYSPLFRPLEGAVQTLFARVAKSLSLTPPPSALEFFLVGLEARHEQGDPLAAVLLGPGEEAALAKEILESRVDALAEVPATGANRLAQVMALWYRMAWTAYYLALLYGVDPGDHGLLE 284
               SCOP domains d1wiwa_ A: Glucose-6-phosphate isomerase-like protein TTHA1346                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh..hhhhhhhhh..............eeeeee..hhhhhhhhh........eeeeee............--......eeeeee......ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..........hhhhhhhhh...hhhhhh.eeeeee..hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wiw A   1 mRDLDREETYLVDRTGLALELRDLVGTGPVPGEAYPGPHAALGYGEGQFAALLSGLPDWGEEGTLFLLEGGYDLGEAAGmA--AETGRARVVRVGFRPGVEVHIPPSPLAPYRYLRFLLLATGREEVLRSVDEALLEERRRLGPEVPVEENPAKFLAYTLLERLPLFYSPLFRPLEGAVQTLFARVAKSLSLTPPPSALEFFLVGLEARHEQGDPLAAVLLGPGEEAALAKEILESRVDALAEVPATGANRLAQVmALWYRmAWTAYYLALLYGVDPGDHGLLE 284
                            |       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     | 260 |     270       280    
                            |                                                                             80-MSE                                                                                                                                                                         256-MSE |                      
                            1-MSE                                                                          81                                                                                                                                                                                  262-MSE                  


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with Q5SIM3_THET8 | Q5SIM3 from UniProtKB/TrEMBL  Length:290

    Alignment length:290
                                    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       260       270       280       290
         Q5SIM3_THET8     1 MRDLDREETYLVDRTGLALELRDLVGTGPVPGEAYPGPHAALGYGEGQFAALLSGLPDWGEEGTLFLLEGGYDLGEAAGMALLAETGRARVVRVGFRPGVEVHIPPSPLAPYRYLRFLLLATGREEVLRSVDEALLEERRRLGPEVPVEENPAKFLAYTLLERLPLFYSPLFRPLEGAVQTLFARVAKSLSLTPPPSALEFFLVGLEARHEQGDPLAAVLLGPGEEAALAKEILESRVDALAEVPATGANRLAQVMALWYRMAWTAYYLALLYGVDPGDHGLLERLREVT 290
               SCOP domains d1wiwb_ B: Glucose-6-phosphate isomerase-like protein TTHA1346                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------  -----------------------------------------------------------bact-PGI_C-1wiwB01 B:146-290                                                                                                                      Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------  -----------------------------------------------------------bact-PGI_C-1wiwB02 B:146-290                                                                                                                      Pfam domains (2)
         Sec.struct. author .....hhhhhh....hhhhhhhhh..............eeeeeee.hhhhhhhhh........eeeeeee....hhhhhhhhhh--...eeeeee......ee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..........hhhhhhhhh..-----...eeeeee..hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wiw B   1 mRDLDREETYLVDRTGLALELRDLVGTGPVPGEAYPGPHAALGYGEGQFAALLSGLPDWGEEGTLFLLEGGYDLGEAAGmALLA--GRARVVRVGFRPGVEVHIPPSPLAPYRYLRFLLLATGREEVLRSVDEALLEERRRLGPEVPVEENPAKFLAYTLLERLPLFYSPLFRPLEGAVQTLFARVAKSLSLTPPPSALEFFLVGLE-----GDPLAAVLLGPGEEAALAKEILESRVDALAEVPATGANRLAQVmALWYRmAWTAYYLALLYGVDPGDHGLLERLREVT 290
                            |       10        20        30        40        50        60        70        80   |  | 90       100       110       120       130       140       150       160       170       180       190       200      |  -  |    220       230       240       250     | 260 |     270       280       290
                            1-MSE                                                                         80-MSE 87                                                                                                                     207   213                                        256-MSE |                            
                                                                                                                                                                                                                                                                                               262-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: bact-PGI_C] (4)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SIM3_THET8 | Q5SIM3)
molecular function
    GO:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    GO:0004476    mannose-6-phosphate isomerase activity    Catalysis of the reaction: D-mannose 6-phosphate = D-fructose 6-phosphate.
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/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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1wiw)
 
  Cis Peptide Bonds
    Gly A:37 - Pro A:38   [ RasMol ]  
    Gly B:37 - Pro B:38   [ RasMol ]  
 

(-) 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 ](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
  1wiw
    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
  Q5SIM3_THET8 | Q5SIM3
    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
  Q5SIM3_THET8 | Q5SIM3
    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 1WIW)

(-) Related Entries Specified in the PDB File

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