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 :  CRYSTAL STRUCTURE OF OXIDOREDUCTASE (TM0312) FROM THERMOTOGA MARITIMA AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Apr 05  (Deposition) - 10 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm0312, Oxidoreductase (Ec 1. 1. 1. -), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Oxidoreductase (Tm0312) From Thermotog Maritima At 2. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OXIDOREDUCTASE
    Chains: A, B
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0312
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:211 , SER A:213 , LEU A:216 , GLY A:218 , ASP A:220BINDING SITE FOR RESIDUE NA A 329
2AC2SOFTWAREASP B:211 , SER B:213 , LEU B:216 , GLY B:218 , ASP B:220BINDING SITE FOR RESIDUE NA B 329
3AC3SOFTWAREGLY A:13 , CYS A:14 , GLY A:15 , ILE A:16 , ALA A:17 , LEU A:21 , SER A:40 , ARG A:41 , THR A:42 , HIS A:45 , THR A:77 , LEU A:78 , PRO A:79 , LEU A:82 , GLU A:100 , LYS A:101 , PRO A:102 , ASN A:129 , TYR A:168 , THR A:171 , TRP A:173 , ARG A:174 , HIS A:190 , TYR A:279 , HOH A:426 , HOH A:459 , HOH A:471 , HOH A:473 , HOH A:485BINDING SITE FOR RESIDUE NAP A 400
4AC4SOFTWAREGLY B:13 , CYS B:14 , GLY B:15 , ILE B:16 , ALA B:17 , LEU B:21 , SER B:40 , ARG B:41 , THR B:42 , HIS B:45 , THR B:77 , LEU B:78 , PRO B:79 , LEU B:82 , GLU B:100 , LYS B:101 , ASN B:129 , TYR B:168 , THR B:171 , TRP B:173 , ARG B:174 , ASP B:186 , HIS B:190 , TYR B:279BINDING SITE FOR RESIDUE NAP B 400
5AC5SOFTWAREHIS A:132 , LYS A:281BINDING SITE FOR RESIDUE EDO A 401
6AC6SOFTWARELYS A:243 , THR B:251 , GLY B:252 , GLY B:255BINDING SITE FOR RESIDUE EDO A 402
7AC7SOFTWAREHIS A:96 , GLU A:121 , LYS A:122 , THR A:123 , VAL A:290BINDING SITE FOR RESIDUE EDO A 403
8AC8SOFTWAREGLU A:246 , TRP A:261BINDING SITE FOR RESIDUE EDO A 404
9AC9SOFTWAREASN A:245 , HOH A:472BINDING SITE FOR RESIDUE EDO A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZH8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:101 -Pro A:102
2Lys B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZH8)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZH8)

(-) 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:325
 aligned with Q9WYE8_THEMA | Q9WYE8 from UniProtKB/TrEMBL  Length:328

    Alignment length:325
                                    13        23        33        43        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     
         Q9WYE8_THEMA     4 LRKIRLGIVGCGIAARELHLPALKNLSHLFEITAVTSRTRSHAEEFAKMVGNPAVFDSYEELLESGLVDAVDLTLPVELNLPFIEKALRKGVHVICEKPISTDVETGKKVVELSEKSEKTVYIAENFRHVPAFWKAKELVESGAIGDPVFMNWQIWVGMDENNKYVHTDWRKKPKHVGGFLSDGGVHHAAAMRLILGEIEWISAVAKDLSPLLGGMDFLSSIFEFENGTVGNYTISYSLKGNERFEITGTKGKISISWDKIVLNEEEMKVPQENSYQKEFEDFYQVVAEGKPNDLGSPVQALKDLAFIEACVRSAGNKVFVSSLL 328
               SCOP domains d1zh8a1 A:4-131,A:276-328 Hypothetical protein TM0312                                                                           d1zh8a2 A:132-275 Hypothetical protein TM0312                                                                                                   d1zh8a1 A:4-131,A:276-328 Hypothetical protein TM0312 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh..eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.eeeeeeeee..........eeeeeeee....eeeeeee.......eeeeee...eeeee..eeee..eeee....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...ee.hhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zh8 A   4 LRKIRLGIVGCGIAARELHLPALKNLSHLFEITAVTSRTRSHAEEFAKmVGNPAVFDSYEELLESGLVDAVDLTLPVELNLPFIEKALRKGVHVICEKPISTDVETGKKVVELSEKSEKTVYIAENFRHVPAFWKAKELVESGAIGDPVFmNWQIWVGmDENNKYVHTDWRKKPKHVGGFLSDGGVHHAAAmRLILGEIEWISAVAKDLSPLLGGmDFLSSIFEFENGTVGNYTISYSLKGNERFEITGTKGKISISWDKIVLNEEEmKVPQENSYQKEFEDFYQVVAEGKPNDLGSPVQALKDLAFIEACVRSAGNKVFVSSLL 328
                                    13        23        33        43        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     
                                                                           52-MSE                                                                                               154-MSE 162-MSE                          195-MSE                 219-MSE                                             271-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q9WYE8_THEMA | Q9WYE8 from UniProtKB/TrEMBL  Length:328

    Alignment length:324
                                    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    
         Q9WYE8_THEMA     5 RKIRLGIVGCGIAARELHLPALKNLSHLFEITAVTSRTRSHAEEFAKMVGNPAVFDSYEELLESGLVDAVDLTLPVELNLPFIEKALRKGVHVICEKPISTDVETGKKVVELSEKSEKTVYIAENFRHVPAFWKAKELVESGAIGDPVFMNWQIWVGMDENNKYVHTDWRKKPKHVGGFLSDGGVHHAAAMRLILGEIEWISAVAKDLSPLLGGMDFLSSIFEFENGTVGNYTISYSLKGNERFEITGTKGKISISWDKIVLNEEEMKVPQENSYQKEFEDFYQVVAEGKPNDLGSPVQALKDLAFIEACVRSAGNKVFVSSLL 328
               SCOP domains d1zh8b1 B:5-131,B:276-328 Hypothetical protein TM0312                                                                          d1zh8b2 B:132-275 Hypothetical protein TM0312                                                                                                   d1zh8b1 B:5-131,B:276-328 Hypothetical protein TM0312 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --GFO_IDH_MocA-1zh8B01 B:7-128                                                                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --GFO_IDH_MocA-1zh8B02 B:7-128                                                                                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhh..ee..hhhhhhh.....eeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhh.....eeeeeeeee.......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.eeeeeeeee..........eeeeeeee....eeeeeee.......eeeeee...eeeee..eeee..eeee....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....ee.hhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zh8 B   5 RKIRLGIVGCGIAARELHLPALKNLSHLFEITAVTSRTRSHAEEFAKmVGNPAVFDSYEELLESGLVDAVDLTLPVELNLPFIEKALRKGVHVICEKPISTDVETGKKVVELSEKSEKTVYIAENFRHVPAFWKAKELVESGAIGDPVFmNWQIWVGmDENNKYVHTDWRKKPKHVGGFLSDGGVHHAAAmRLILGEIEWISAVAKDLSPLLGGmDFLSSIFEFENGTVGNYTISYSLKGNERFEITGTKGKISISWDKIVLNEEEmKVPQENSYQKEFEDFYQVVAEGKPNDLGSPVQALKDLAFIEACVRSAGNKVFVSSLL 328
                                    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    
                                                                          52-MSE                                                                                               154-MSE 162-MSE                          195-MSE                 219-MSE                                             271-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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZH8)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WYE8_THEMA | Q9WYE8)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.
    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 ]
    NAP  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:101 - Pro A:102   [ RasMol ]  
    Lys B:101 - Pro B:102   [ RasMol ]  
 

(-) 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
  1zh8
    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
  Q9WYE8_THEMA | Q9WYE8
    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)
  1.1.1.-
    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
  Q9WYE8_THEMA | Q9WYE8
    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 1ZH8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ZH8)