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

(-) Description

Title :  STRUCTURE OF NADPH-DEPENDENT FAMILY 11 ALDO-KETO REDUCTASE AKR11A(APO)
 
Authors :  A. H. Ehrensberger, D. K. Wilson
Date :  08 Jul 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha Barrel, Aldo-Keto Reductase, Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Ehrensberger, D. K. Wilson
Structural And Catalytic Diversity In The Two Family 11 Aldo-Keto Reductases
J. Mol. Biol. V. 337 661 2004
PubMed-ID: 15019785  |  Reference-DOI: 10.1016/J.JMB.2004.01.059
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IOLS PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: BL21*
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IOLS OR SS92ER
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: VEGETATIVE PROTEIN 147, VEG147

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:268 , ARG A:270 , ILE A:273 , HOH A:343 , HOH A:396 , HOH A:400BINDING SITE FOR RESIDUE NA A 315
2AC2SOFTWAREGLY A:7 , ASN A:197 , ILE A:198 , PRO A:271 , GLU A:272 , ASP A:274 , HOH A:368 , HOH A:378BINDING SITE FOR RESIDUE EDO A 313
3AC3SOFTWAREGLU A:35 , LYS A:38 , ARG A:42 , SER A:303 , PHE A:304 , HOH A:325 , HOH A:347BINDING SITE FOR RESIDUE EDO A 314

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PYF)

(-) 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:311
 aligned with IOLS_BACSU | P46336 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:311
                                                                                                                                                                                                                                                                                                                                              310  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301        |- 
           IOLS_BACSU     2 KKAKLGKSDLQVFPIGLGTNAVGGHNLYPNLNEETGKELVREAIRNGVTMLDTAYIYGIGRSEELIGEVLREFNREDVVIATKAAHRKQGNDFVFDNSPDFLKKSVDESLKRLNTDYIDLFYIHFPDEHTPKDEAVNALNEMKKAGKIRSIGVSNFSLEQLKEANKDGLVDVLQGEYNLLNREAEKTFFPYTKEHNISFIPYFPLVSGLLAGKYTEDTTFPEGDLRNEQEHFKGERFKENIRKVNKLAPIAEKHNVDIPHIVLAWYLARPEIDILIPGAKRADQLIDNIKTADVTLSQEDISFIDKLFA--   -
               SCOP domains d1pyfa_ A: Putative oxidoreductase IolS                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1pyfA00 A:2-312 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee....ee.............hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhhheeeeee.eeee..eeee..hhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhh.....eeee..hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhh.eeeee.....hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pyf A   2 KKAKLGKSDLQVFPIGLGTNAVGGHNLYPNLNEETGKELVREAIRNGVTmLDTAYIYGIGRSEELIGEVLREFNREDVVIATKAAHRKQGNDFVFDNSPDFLKKSVDESLKRLNTDYIDLFYIHFPDEHTPKDEAVNALNEmKKAGKIRSIGVSNFSLEQLKEANKDGLVDVLQGEYNLLNREAEKTFFPYTKEHNISFIPYFPLVSGLLAGKYTEDTTFPEGDLRNEQEHFKGERFKENIRKVNKLAPIAEKHNVDIPHIVLAWYLARPEIDILIPGAKRADQLIDNIKTADVTLSQEDISFIDKLFAPG 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 |     151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
                                                                            51-MSE                                                                                     143-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PYF)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IOLS_BACSU | P46336)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 1pyf)
 

(-) 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 | Asym./Biol. Unit - 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
  1pyf
    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
  IOLS_BACSU | P46336
    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)
  (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
  IOLS_BACSU | P46336
    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
        IOLS_BACSU | P46336: 1pz0

(-) Related Entries Specified in the PDB File

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