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 :  SHEEP LIVER SORBITOL DEHYDROGENASE
 
Authors :  N. H. Yennawar, H. P. Yennawar
Date :  19 Jan 11  (Deposition) - 27 Apr 11  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Medium Chain Dehydrogenase/Reductase Enzymes, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yennawar, M. Moller, R. Gillilan, N. Yennawar
X-Ray Crystal Structure And Small-Angle X-Ray Scattering Of Sheep Liver Sorbitol Dehydrogenase.
Acta Crystallogr. , Sect. D V. 67 440 2011
PubMed-ID: 21543846  |  Reference-DOI: 10.1107/S0907444911007815

(-) Compounds

Molecule 1 - SORBITOL DEHYDROGENASE
    ChainsA
    EC Number1.1.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSORD
    OrganLIVER
    Organism CommonSHEEP
    Organism ScientificOVIS ARIES
    Organism Taxid9940
    SynonymL-IDITOL 2-DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2GOL1Ligand/IonGLYCEROL
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1ACY12Ligand/IonACETIC ACID
2GOL4Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:43 , HIS A:68 , GLU A:69 , GLU A:154 , HOH A:470BINDING SITE FOR RESIDUE ZN A 356
2AC2SOFTWARETYR A:49 , THR A:120 , ARG A:297 , ACY A:359 , HOH A:489BINDING SITE FOR RESIDUE GOL A 357
3AC3SOFTWAREGLN A:197 , ALA A:310 , HOH A:424BINDING SITE FOR RESIDUE ACY A 358
4AC4SOFTWAREHIS A:68 , GLU A:154 , VAL A:158 , GOL A:357 , HOH A:470 , HOH A:489BINDING SITE FOR RESIDUE ACY A 359
5AC5SOFTWAREGLU A:32 , HIS A:133 , ASN A:134BINDING SITE FOR RESIDUE ACY A 360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QE3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QE3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.DHSO_SHEEP66-80  1A:67-81
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_ZINCPS00059 Zinc-containing alcohol dehydrogenases signature.DHSO_SHEEP66-80  4A:67-81

(-) Exons   (0, 0)

(no "Exon" information available for 3QE3)

(-) 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:351
 aligned with DHSO_SHEEP | P07846 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:351
                                                                           52                                                                                                                                                                                                                                                                                                              
                                                                         51 |                                                                                                                                                                                                                                                                                                              
                                    14        24        34        44      | 53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353 
           DHSO_SHEEP     5 AENLSLVVHGPGDLRLENYPIPEPGPNEVLLKMHSVGICGSDVHYWQ-GRIGDFVVKKPMVLGHEASGTVVKVGSLVRHLQPGDRVAIQPGAPRQTDEFCKIGRYNLSPTIFFCATPPDDGNLCRFYKHNANFCYKLPDNVTFEEGALIEPLSVGIHACRRAGVTLGNKVLVCGAGPIGLVNLLAAKAMGAAQVVVTDLSASRLSKAKEVGADFILEISNESPEEIAKKVEGLLGSKPEVTIECTGVETSIQAGIYATHSGGTLVLVGLGSEMTSVPLVHAATREVDIKGVFRYCNTWPMAISMLASKSVNVKPLVTHRFPLEKALEAFETSKKGLGLKVMIKCDPSDQNP 354
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------ADH_N-3qe3A01 A:30-141                                                                                          ---------------------------------------ADH_zinc_N-3qe3A02 A:181-311                                                                                                       -------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeee.........eeeeeeeeeeehhhhhhhhhhhee..ee....ee...eeeeeeeee...........eeee..ee....hhhhhh.hhhhh...ee............eeeee...eee.....hhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....eeee..........hhhhhhhh..eeee......hhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhhh...eeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------ADH_ZINC       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qe3 A   5 AENLSLVVHGPGDLRLENYPIPEPGPNEVLLKMHSVGICGSDVHYWQHGRIGDFVVKKPMVLGHEASGTVVKVGSLVRHLQPGDRVAIQPGAPRQTDEFCKIGRYNLSPTIFFCATPPDDGNLCRFYKHNANFCYKLPDNVTFEEGALIEPLSVGIHACRRAGVTLGNKVLVCGAGPIGLVNLLAAKAMGAAQVVVTDLSASRLSKAKEVGADFILEISNESPEEIAKKVEGLLGSKPEVTIECTGVETSIQAGIYATHSGGTLVLVGLGSEMTSVPLVHAATREVDIKGVFRYCNTWPMAISMLASKSVNVKPLVTHRFPLEKALEAFETSKKGLGLKVMIKCDPSDQNP 355
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354 

   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  (0, 0)

(no "SCOP Domain" information available for 3QE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QE3)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GroES (70)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (DHSO_SHEEP | P07846)
molecular function
    GO:0003939    L-iditol 2-dehydrogenase activity    Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030317    flagellated sperm motility    Any process involved in the controlled movement of a flagellated sperm cell.
    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.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.

 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
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Pro A:121 - Pro A:122   [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qe3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DHSO_SHEEP | P07846
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.14
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DHSO_SHEEP | P07846
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DHSO_SHEEP | P078461sdg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QE3)