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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE B RPIB FROM GIARDIA LAMBLIA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  23 May 11  (Deposition) - 01 Jun 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Giardia, Isomerase, Ribose-5-Phosphate, Ribulose-5-Phosphate, Rpib, Rpia, Pentose Phosphate Pathway, Pentose-Phosphate Shunt, Flagellated Protozoan Parasite, Gastrointestinal Tract Parasite (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, J. Abendroth, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Ribose-5-Phosphate Isomerase B Rpib From Giardia Lamblia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: GL50803_27614
    Organism Scientific: GIARDIA LAMBLIA
    Organism Taxid: 184922
    Strain: ATCC 50803 WB C6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:65 , GLY A:66 , THR A:67 , GLY A:68 , ILE A:69 , GLY A:70 , ILE A:71 , HOH A:153 , HOH A:167 , ASN B:99BINDING SITE FOR RESIDUE SO4 A 146
2AC2SOFTWARELYS A:77 , MET B:78 , LYS B:79 , GLY B:80BINDING SITE FOR RESIDUE SO4 A 147
3AC3SOFTWAREGLY A:80 , ARG A:82 , ARG B:12 , ARG B:15 , GLY B:33 , THR B:34 , LYS B:77 , HOH B:153 , HOH B:154BINDING SITE FOR RESIDUE SO4 B 146
4AC4SOFTWAREASN A:99 , GLY B:66 , THR B:67 , GLY B:68 , ILE B:69 , GLY B:70 , HOH B:169BINDING SITE FOR RESIDUE SO4 B 147
5AC5SOFTWAREGLY A:130 , GLY A:131 , HOH A:164 , PHE B:17 , GLN B:20 , ARG B:21BINDING SITE FOR RESIDUE SO4 B 148

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S5P)

(-) Exons   (0, 0)

(no "Exon" information available for 3S5P)

(-) 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:134
 aligned with A8B2K2_GIAIC | A8B2K2 from UniProtKB/TrEMBL  Length:145

    Alignment length:142
                               1                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137  
         A8B2K2_GIAIC     - ---MKVAFASDHGGRDLRMFLQQRASAHGYEVMDLGTESDASVDYPDFAKIGCEAVTSGRADCCILVCGTGIGISIAANKMKGIRCALCSTEYDAEMARKHNNANALALGGRTTGPEVAASILSRFLSTNFEGGRHAARIAK 139
               SCOP domains d3s5pa_ A: automated matches                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhh..eeeeee.--------hhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh..hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5p A  -2 PGSMKVAFASDHGGRDLRMFLQQRASAHGYEVMDLGT--------PDFAKIGCEAVTSGRADCCILVCGTGIGISIAANKMKGIRCALCSTEYDAEMARKHNNANALALGGRTTGPEVAASILSRFLSTNFEGGRHAARIAK 139
                                     7        17        27      |  -     |  47        57        67        77        87        97       107       117       127       137  
                                                               34       43                                                                                                


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with A8B2K2_GIAIC | A8B2K2 from UniProtKB/TrEMBL  Length:145

    Alignment length:132
                               1                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127  
         A8B2K2_GIAIC     - ---MKVAFASDHGGRDLRMFLQQRASAHGYEVMDLGTESDASVDYPDFAKIGCEAVTSGRADCCILVCGTGIGISIAANKMKGIRCALCSTEYDAEMARKHNNANALALGGRTTGPEVAASILSRFLSTNFE 129
               SCOP domains d3s5pb_ B: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----LacAB_rpiB-3s5pB01 B:2-129                                                                                                       Pfam domains (1)
           Pfam domains (2) ----LacAB_rpiB-3s5pB02 B:2-129                                                                                                       Pfam domains (2)
         Sec.struct. author ....eeeeee...hhhhhhhhhhhhhhh..eeeeeee.-------hhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3s5p B  -2 PGSMKVAFASDHGGRDLRMFLQQRASAHGYEVMDLGTE-------PDFAKIGCEAVTSGRADCCILVCGTGIGISIAANKMKGIRCALCSTEYDAEMARKHNNANALALGGRTTGPEVAASILSRFLSTNFE 129
                                     7        17        27       | -     |  47        57        67        77        87        97       107       117       127  
                                                                35      43
   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  (0, 0)

(no "CATH Domain" information available for 3S5P)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: LacAB_rpiB] (12)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A8B2K2_GIAIC | A8B2K2)
molecular function
    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:0004751    ribose-5-phosphate isomerase activity    Catalysis of the reaction: D-ribose 5-phosphate = D-ribulose 5-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.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

 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
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3s5p)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  3s5p
    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
  A8B2K2_GIAIC | A8B2K2
    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)
  5.3.1.6
    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
  A8B2K2_GIAIC | A8B2K2
    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 3S5P)

(-) Related Entries Specified in the PDB File

3qd5 RPIB FROM COCCIDIOIDES IMMITIS RELATED ID: GILAA.01163.A RELATED DB: TARGETDB