Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 PHOSPHOGLYCERATE MUTASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Sugahara, S. Yokoyama, S. Kuramitsu, M. Miyano, T. Iizuka, N. Kunish Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Oct 03  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphoglycerate Mutase, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, S. Yokoyama, S. Kuramitsu, M. Miyano, T. Iizuka, N. Kunishima
Crystal Structure Of Phosphoglycerate Mutase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE MUTASE
    Chains: A, B
    EC Number: 5.4.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:120 , GLY A:123 , LEU A:124 , HOH A:1097 , HOH A:1126 , HOH A:1161BINDING SITE FOR RESIDUE GOL A 1001
2AC2SOFTWAREARG B:67 , PHE B:120 , GLY B:123 , LEU B:124 , HOH B:1108 , HOH B:1175 , HOH B:1180BINDING SITE FOR RESIDUE GOL B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V37)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:160 -Pro A:161
2Trp B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V37)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V37)

(-) Exons   (0, 0)

(no "Exon" information available for 1V37)

(-) 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:171
 aligned with Q53WB3_THET8 | Q53WB3 from UniProtKB/TrEMBL  Length:177

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
         Q53WB3_THET8     1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLALD 171
               SCOP domains d1v37a_ A: Alpha-ribazole-5'-phosphate phosphatase                                                                                                                          SCOP domains
               CATH domains 1v37A00 A:1-171 Phosphoglycerate mutase-like                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhh..........hhhhhhhhhhhh.......eee..hhhhhhhhhhh....ee.hhhh...hhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh..........eeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v37 A   1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLALD 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q53WB3_THET8 | Q53WB3 from UniProtKB/TrEMBL  Length:177

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q53WB3_THET8     1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLAL 170
               SCOP domains d1v37b_ B: Alpha-ribazole-5'-phosphate phosphatase                                                                                                                         SCOP domains
               CATH domains 1v37B00 B:1-170 Phosphoglycerate mutase-like                                                                                                                               CATH domains
           Pfam domains (1) -His_Phos_1-1v37B01 B:2-140                                                                                                                 ------------------------------ Pfam domains (1)
           Pfam domains (2) -His_Phos_1-1v37B02 B:2-140                                                                                                                 ------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhh..........hhhhhhhhhhhh.......eee..hhhhhhhhhhh....ee.hhhh...hhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh..........eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v37 B   1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLAL 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q53WB3_THET8 | Q53WB3)
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:160 - Pro A:161   [ RasMol ]  
    Trp B:160 - Pro B:161   [ RasMol ]  
 
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
  1v37
    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
  Q53WB3_THET8 | Q53WB3
    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)
  5.4.2.1
    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
  Q53WB3_THET8 | Q53WB3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q53WB3_THET8 | Q53WB3: 1v7q 2ekb 2ekz 2enu 2enw 2eoa 2hia 2owd 2owe 2p2y 2p2z 2p30 2p6m 2p6o 2p75 2p77 2p78 2p79 2p9f 2p9y 2p9z 2pa0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V37)