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
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)

(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF OXIDOREDUCTASE
 
Authors :  N. Kamiya, T. Hikima, A. Ebihara, Y. Inoue, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Mar 07  (Deposition) - 11 Mar 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Rossmann Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kamiya, T. Hikima, A. Ebihara, Y. Inoue
Crystal Structure Analysis Of Putative Oxidoreductase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE, SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:12 , SER A:14BINDING SITE FOR RESIDUE CO A 1001
2AC2SOFTWARESER B:14 , ARG B:37 , ASP B:38BINDING SITE FOR RESIDUE CO B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EHD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EHD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EHD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EHD)

(-) Exons   (0, 0)

(no "Exon" information available for 2EHD)

(-) 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:207
 aligned with Q5SK86_THET8 | Q5SK86 from UniProtKB/TrEMBL  Length:234

    Alignment length:223
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
         Q5SK86_THET8     4 MKGAVLITGASRGIGEATARLLHAKGYRVGLMARDEKRLQALAAELEGALPLPGDVREEGDWARAVAAMEEAFGELSALVNNAGVGVMKPVHELTLEEWRLVLDTNLTGAFLGIRHAVPALLRRGGGTIVNVGSLAGKNPFKGGAAYNASKFGLLGLAGAAMLDLREANVRVVNVLPGSVDTGFAGNTPGQAWKLKPEDVAQAVLFALEMPGHAMVSEIELRP 226
               SCOP domains d2ehda_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..----------------.hhhhhhhhhhhhhhh.......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehd A   4 MKGAVLITGASRGIGEATARLLHAKGYRVGLMARDEKRLQALAAELEGALPLPGDVREEGDWARAVAAMEEAFGELSALVNNAGVGVMKPVHELTLEEWRLVLDTNLTGAFLGIRHAVPALLRRGGGTIVNVGSLAGKNPFKGGAAYNASKFGLLGLAGAAMLDLREANVRVVNVLPG----------------LKPEDVAQAVLFALEMPGHAMVSEIELRP 226
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       | -         -    |  203       213       223   
                                                                                                                                                                                                           181              198                            


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q5SK86_THET8 | Q5SK86 from UniProtKB/TrEMBL  Length:234

    Alignment length:226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
         Q5SK86_THET8     2 EGMKGAVLITGASRGIGEATARLLHAKGYRVGLMARDEKRLQALAAELEGALPLPGDVREEGDWARAVAAMEEAFGELSALVNNAGVGVMKPVHELTLEEWRLVLDTNLTGAFLGIRHAVPALLRRGGGTIVNVGSLAGKNPFKGGAAYNASKFGLLGLAGAAMLDLREANVRVVNVLPGSVDTGFAGNTPGQAWKLKPEDVAQAVLFALEMPGHAMVSEIELRPT 227
               SCOP domains d2ehdb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...-------------..hhhhhhhhhhhhhh........eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehd B   2 EGMKGAVLITGASRGIGEATARLLHAKGYRVGLMARDEKRLQALAAELEGALPLPGDVREEGDWARAVAAMEEAFGELSALVNNAGVGVMKPVHELTLEEWRLVLDTNLTGAFLGIRHAVPALLRRGGGTIVNVGSLAGKNPFKGGAAYNASKFGLLGLAGAAMLDLREANVRVVNVLPGSV-------------KLKPEDVAQAVLFALEMPGHAMVSEIELRPT 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 |       -     | 201       211       221      
                                                                                                                                                                                                               183           197
   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 2EHD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EHD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SK86_THET8 | Q5SK86)
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 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
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ehd)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2ehd
    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
  Q5SK86_THET8 | Q5SK86
    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)
  (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
  Q5SK86_THET8 | Q5SK86
    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 2EHD)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EHD)