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
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - 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)

(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS WITH BOUND 5-PHOSPHO-D-ARABINONATE
 
Authors :  J. M. Berrisford, J. Akerboom, S. Brouns, S. E. Sedelnikova, A. P. Turnb Der Oost, L. Salmon, R. Hardre, I. A. Murray, G. M. Blackburn, D. W. Ric P. J. Baker
Date :  17 Aug 04  (Deposition) - 12 Oct 04  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cupin Superfamily, Pyrococcus Furiosus, Hyperthermophile, Phosphoglucose Isomerase, Extremeophile, 5-Phospho-D-Arabinonate, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Berrisford, J. Akerboom, S. Brouns, S. E. Sedelnikova, A. P. Turnbull, J. Van Der Oost, L. Salmon, R. Hardre, I. A. Murray, G. M. Blackburn, D. W. Rice, P. J. Baker
The Structures Of Inhibitor Complexes Of Pyrococcus Furiosu Phosphoglucose Isomerase Provide Insights Into Substrate Binding And Catalysis.
J. Mol. Biol. V. 343 649 2004
PubMed-ID: 15465052  |  Reference-DOI: 10.1016/J.JMB.2004.08.061

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
    Chains: A
    EC Number: 5.3.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24-D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PGIA
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: GPI, PHOSPHOGLUCOSE ISOMERASE, PGI, PHOSPHOHEXOSE ISOMERASE, PHI

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2PA51Ligand/Ion5-PHOSPHOARABINONIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PA52Ligand/Ion5-PHOSPHOARABINONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:52 , THR A:71 , THR A:85 , LYS A:86 , GLY A:87 , HIS A:88 , GLU A:97 , TYR A:99 , HIS A:136 , PHE A:148 , ALA A:150 , TYR A:152 , TYR A:160 , HOH A:302 , HOH A:303 , HOH A:304 , HOH A:305 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE PA5 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X82)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X82)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X82)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X82)

(-) Exons   (0, 0)

(no "Exon" information available for 1X82)

(-) 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:190
 aligned with G6PI_PYRFU | P83194 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:190
                             1                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
           G6PI_PYRFU     - -MYKEPFGVKVDFETGIIEGAKKSVRRLSDMEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGMLLQTPEGDAKWISMEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRWKK 189
               SCOP domains d1x82a_ A: Glucose-6-phosphate isomerase, GPI                                                                                                                                                  SCOP domains
               CATH domains --1x82A00 A:2-189 Jelly Rolls                                                                                                                                                                  CATH domains
               Pfam domains ------------------------GPI-1x82A01 A:24-188                                                                                                                                                 - Pfam domains
         Sec.struct. author ......................eeeee.hhhh....hhhhhhhhhhhh..eeeeeeee........eeeeeeee...ee..ee..............eeeeeee..eeeeee.....eeeeee....eeee....eeeeee.....eeeeeeee......hhhhhhhh..eeeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x82 A   0 mmYKEPFGVKVDFETGIIEGAKKSVRRLSDmEGYFVDERAWKELVEKEDPVVYEVYAVEQEEKEGDLNFATTVLYPGKVGKEFFFTKGHFHAKLDRAEVYVALKGKGGmLLQTPEGDAKWISmEPGTVVYVPPYWAHRTVNIGDEPFIFLAIYPADAGHDYGTIAEKGFSKIVIEENGEVKVVDNPRWKK 189
                            ||       9        19        29|       39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189
                            ||                           30-MSE                                                                       108-MSE       122-MSE                                                               
                            0-MSE                                                                                                                                                                                         
                             1-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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (G6PI_PYRFU | P83194)
molecular function
    GO:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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 ]
    PA5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x82)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1x82
    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
  G6PI_PYRFU | P83194
    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)
  5.3.1.9
    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
  G6PI_PYRFU | P83194
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_PYRFU | P83194: 1qxj 1qxr 1qy4 1x7n 1x8e 2gc0 2gc1 2gc2 2gc3 3sxw 4lta 4luk 4lul 4lum

(-) Related Entries Specified in the PDB File

1plz