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 :  NADH OXIDASE FROM THERMUS THERMOPHILUS
 
Authors :  H. J. Hecht, H. Erdmann, H. J. Park, M. Sprinzl, R. D. Schmid
Date :  20 Nov 96  (Deposition) - 12 Mar 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoenzyme, Flavoprotein Fmn, Oxidoreductase, Thermophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Hecht, H. Erdmann, H. J. Park, M. Sprinzl, R. D. Schmid
Crystal Structure Of Nadh Oxidase From Thermus Thermophilus
Nat. Struct. Biol. V. 2 1109 1995
PubMed-ID: 8846223  |  Reference-DOI: 10.1038/NSB1295-1109

(-) Compounds

Molecule 1 - NADH OXIDASE
    Atcc: 27634
    Chains: A
    EC Number: 1.6.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTNADOX
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector: PKK223-3
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , ARG A:18 , SER A:19 , ARG A:21 , PRO A:44 , SER A:45 , ALA A:46 , ASN A:48 , GLN A:73 , GLN A:135 , PRO A:156 , MET A:157 , LEU A:158 , GLY A:159 , SER A:193 , ARG A:195 , HOH A:302 , HOH A:303 , HOH A:311 , HOH A:353 , HOH A:373BINDING SITE FOR RESIDUE FMN A 300
2COFUNKNOWNFMN A:300COFACTOR

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NOX)

(-) 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:200
 aligned with NOX_THET8 | Q60049 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
            NOX_THET8     6 PVLDAKTAALKRRSIRRYRKDPVPEGLLREILEAALRAPSAWNLQPWRIVVVRDPATKRALREAAFGQAHVEEAPVVLVLYADLEDALAHLDEVIHPGVQGERREAQKQAIQRAFAAMGQEARKAWASGQSYILLGYLLLLLEAYGLGSVPMLGFDPERVRAILGLPSHAAIPALVALGYPAEEGYPSHRLPLERVVLWR 205
               SCOP domains d1noxa_ A: NADH oxidase                                                                                                                                                                                  SCOP domains
               CATH domains 1noxA00 A:6-205 NADH Oxidase                                                                                                                                                                             CATH domains
               Pfam domains --------Nitroreductase-1noxA01 A:14-185                                                                                                                                             -------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.............hhhhhhhhhhhhh...hhh...eeeeee..hhhhhhhhhh....hhhhh..eeeeeee.hhhhhhhhhh........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh.........eeeeee.............hhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nox A   6 PVLDAKTAALKRRSIRRYRKDPVPEGLLREILEAALRAPSAWNLQPWRIVVVRDPATKRALREAAFGQAHVEEAPVVLVLYADLEDALAHLDEVIHPGVQGERREAQKQAIQRAFAAMGQEARKAWASGQSYILLGYLLLLLEAYGLGSVPMLGFDPERVRAILGLPSRAAIPALVALGYPAEEGYPSHRLPLERVVLWR 205
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Nitroreductase] (9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (NOX_THET8 | Q60049)
molecular function
    GO:0003954    NADH dehydrogenase activity    Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
    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
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    COF  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nox)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1nox
    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
  NOX_THET8 | Q60049
    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)
  1.6.99.3
    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
  NOX_THET8 | Q60049
    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 1NOX)

(-) Related Entries Specified in the PDB File

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