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 :  PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT WITH BOUND NADP+
 
Authors :  T. H. Tahirov, E. Inagaki, H. Takahashi
Date :  21 Nov 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxygenase, Fmn-Binding Protein, Structural Genomics, Monooxygenase, Nadp, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takahashi, E. Inagaki, T. H. Tahirov
Crystal Structure Of Putative Styrene Monooxygenase Small Component From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FMN BINDING DOMAIN
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: THE PROTEIN WAS ISOLATED WITH BOUND FMN
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL2Ligand/IonGLYCEROL
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:33 , CYS A:35 , PRO A:36 , ALA A:37 , VAL A:38 , TRP A:39 , SER A:53 , ILE A:54 , SER A:55 , ARG A:58 , PHE A:59 , THR A:60 , LEU A:86 , GLY A:87 , HIS A:89 , SER A:90 , GLY A:91 , LYS A:96 , HIS A:131 , TYR A:162 , TYR A:168 , NAP A:1180 , GOL A:1182 , HOH A:2174 , HOH A:2175 , HOH A:2176BINDING SITE FOR RESIDUE FMN A1179
2AC2SOFTWARETYR A:14 , TYR A:17 , ARG A:58 , HIS A:84 , TYR A:162 , GLY A:164 , LYS A:165 , GLY A:166 , FMN A:1179 , GOL A:1182 , HOH A:2089 , HOH A:2177 , HOH A:2178 , HOH A:2179 , HOH A:2180 , GLU B:30BINDING SITE FOR RESIDUE NAP A1180
3AC3SOFTWARESER A:3 , ARG A:5 , HOH A:2181 , HOH A:2182 , HOH A:2183 , HIS B:105 , VAL B:139BINDING SITE FOR RESIDUE NAP A1181
4AC4SOFTWAREASN B:33 , CYS B:35 , PRO B:36 , ALA B:37 , VAL B:38 , TRP B:39 , SER B:53 , ILE B:54 , SER B:55 , ARG B:58 , PHE B:59 , THR B:60 , LEU B:86 , GLY B:87 , HIS B:89 , SER B:90 , GLY B:91 , LYS B:96 , HIS B:131 , TYR B:162 , TYR B:168 , NAP B:1180 , GOL B:1182 , HOH B:2149 , HOH B:2150 , HOH B:2151BINDING SITE FOR RESIDUE FMN B1179
5AC5SOFTWAREGLU A:30 , TYR B:14 , TYR B:17 , ARG B:58 , HIS B:84 , SER B:88 , TYR B:162 , GLY B:164 , LYS B:165 , GLY B:166 , FMN B:1179 , GOL B:1182 , HOH B:2085 , HOH B:2152 , HOH B:2153 , HOH B:2154BINDING SITE FOR RESIDUE NAP B1180
6AC6SOFTWAREHIS A:105 , VAL A:139 , HOH A:2096 , SER B:3 , TYR B:4 , ARG B:5 , HOH B:2155 , HOH B:2156 , HOH B:2157BINDING SITE FOR RESIDUE NAP B1181
7AC7SOFTWAREVAL A:38 , TRP A:39 , ARG A:58 , HIS A:131 , FMN A:1179 , NAP A:1180 , HOH A:2184 , HOH A:2185BINDING SITE FOR RESIDUE GOL A1182
8AC8SOFTWAREVAL B:38 , TRP B:39 , ARG B:58 , HIS B:131 , FMN B:1179 , NAP B:1180 , HOH B:2158 , HOH B:2159BINDING SITE FOR RESIDUE GOL B1182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:17 -Pro A:18
2Asp A:46 -Pro A:47
3Tyr B:17 -Pro B:18
4Asp B:46 -Pro B:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1USF)

(-) 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:178
 aligned with P83818_THETH | P83818 from UniProtKB/TrEMBL  Length:178

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
         P83818_THETH     1 MRSYRAQGPLPGFYHYYPGVPAVVGVRVEERVNFCPAVWNTGLSADPPLFGVSISPKRFTHGLLLKARRFSASFHPFGQKDLVHWLGSHSGREVDKGQAPHFLGHTGVPILEGAYAAYELELLEVHTFGDHDLFVGRVVAVWEEEGLLDEKGRPKPGLALLYYGKGLYGRPAEETFAP 178
               SCOP domains d1usfa_ A: Putative styrene monooxygenase small component                                                                                                                          SCOP domains
               CATH domains 1usfA00 A:1-178 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee................eeeeeee..eeeeeee..eeeee....eeeeee...hhhhhhhhhhheeeeee....hhhhhhhhh.......hhhhh.eee.....eee....eeeeeeeeeeeee..eeeeeeeeeeeee.................eeee..eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usf A   1 MRSYRAQGPLPGFYHYYPGVPAVVGVRVEERVNFCPAVWNTGLSADPPLFGVSISPKRFTHGLLLKARRFSASFHPFGQKDLVHWLGSHSGREVDKGQAPHFLGHTGVPILEGAYAAYELELLEVHTFGDHDLFVGRVVAVWEEEGLLDEKGRPKPGLALLYYGKGLYGRPAEETFAP 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with P83818_THETH | P83818 from UniProtKB/TrEMBL  Length:178

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
         P83818_THETH     1 MRSYRAQGPLPGFYHYYPGVPAVVGVRVEERVNFCPAVWNTGLSADPPLFGVSISPKRFTHGLLLKARRFSASFHPFGQKDLVHWLGSHSGREVDKGQAPHFLGHTGVPILEGAYAAYELELLEVHTFGDHDLFVGRVVAVWEEEGLLDEKGRPKPGLALLYYGKGLYGRPAEETFAP 178
               SCOP domains d1usfb_ B: Putative styrene monooxygenase small component                                                                                                                          SCOP domains
               CATH domains 1usfB00 B:1-178 Electron Transport, Fmn-binding Protein; Chain A                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee................eeeeeee..eeeeeee..eeeee....eeeeee...hhhhhhhhhhheeeeee....hhhhhhhhh.......hhhhh.eee.....eee....eeeeeeeeeeeee..eeeeeeeeeeeee.hhh.............eeee..eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1usf B   1 MRSYRAQGPLPGFYHYYPGVPAVVGVRVEERVNFCPAVWNTGLSADPPLFGVSISPKRFTHGLLLKARRFSASFHPFGQKDLVHWLGSHSGREVDKGQAPHFLGHTGVPILEGAYAAYELELLEVHTFGDHDLFVGRVVAVWEEEGLLDEKGRPKPGLALLYYGKGLYGRPAEETFAP 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83818_THETH | P83818)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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: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
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:46 - Pro A:47   [ RasMol ]  
    Asp B:46 - Pro B:47   [ RasMol ]  
    Tyr A:17 - Pro A:18   [ RasMol ]  
    Tyr B:17 - Pro B:18   [ 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
  1usf
    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
  P83818_THETH | P83818
    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
  P83818_THETH | P83818
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P83818_THETH | P83818: 1usc

(-) Related Entries Specified in the PDB File

1usc PUTATIVE STYRENE MONOOXYGENASE SMALL COMPONENT