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 FLAVOPROTEIN (TM0755) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  21 Sep 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm0755, Flavoprotein, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Flavoprotein (Tm0755) From Thermotoga Maritima At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FLAVOPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0755
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FEO2Ligand/IonMU-OXO-DIIRON
4MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:327 , ARG B:327BINDING SITE FOR RESIDUE CL A 399
2AC2SOFTWAREMSE A:263 , TYR A:264 , GLY A:265 , PHE A:266 , VAL A:267 , TYR A:318BINDING SITE FOR RESIDUE CL A 400
3AC3SOFTWAREMSE B:263 , TYR B:264 , GLY B:265 , PHE B:266 , VAL B:267 , TYR B:318BINDING SITE FOR RESIDUE CL B 399
4AC4SOFTWAREHIS A:85 , GLU A:87 , ASP A:89 , HIS A:90 , HIS A:151 , ASP A:168 , HIS A:228 , HOH A:408BINDING SITE FOR RESIDUE FEO A 401
5AC5SOFTWAREHIS B:85 , GLU B:87 , ASP B:89 , HIS B:90 , HIS B:151 , ASP B:168 , HIS B:228 , HOH B:407BINDING SITE FOR RESIDUE FEO B 400
6AC6SOFTWAREGLY A:119 , LYS B:377 , GLY B:378BINDING SITE FOR RESIDUE EDO B 401
7AC7SOFTWARELYS A:377 , GLY A:378BINDING SITE FOR RESIDUE EDO A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:12 -Pro A:13
2Leu A:150 -His A:151
3Asp B:12 -Pro B:13
4Leu B:150 -His B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VME)

(-) 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:402
 aligned with Q9WZL4_THEMA | Q9WZL4 from UniProtKB/TrEMBL  Length:398

    Alignment length:402
                                1                                                                                                                                                                                                                                                                                                                                                                                                             
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
         Q9WZL4_THEMA     - ----MPKIWTERIFDDPEIYVLRIDDDRIRYFEAVWEIPEGISYNAYLVKLNGANVLIDGWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKTIGHDVEIIASNFGKRLLEGFYGIKDVTVVKDGEEREIGGKKFKFVMTPWLHWPDTMVTYLDGILFSCDVGGGYLLPEILDDSNESVVERYLPHVTKYIVTVIGHYKNYILEGAEKLSSLKIKALLPGHGLIWKKDPQRLLNHYVSVAKGDPKKGKVTVIYDSMYGFVENVMKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSEALIFGVSTYEAEIHPLMRFTLLEIIDKANYEKPVLVFGVHGWAPSAERTAGELLKETKFRILSFTEIKGSNMDERKIEEAISLLKKELE 398
               SCOP domains ----d1vmea2 A:1-250 ROO-like flavoprotein TM0755, N-terminal domain                                                                                                                                                                                           d1vmea1 A:251-398 ROO-like flavoprotein TM0755, C-terminal domain                                                                                    SCOP domains
               CATH domains 1vmeA01 A:-3-249 Metallo-beta-lactamase, chain A                                                                                                                                                                                                             1vmeA02 A:250-398  [code=3.40.50.360, no name defined]                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee...eeeeeeeee....eehhhee....eeeeeeeee....eeee...hhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh....ee.....eeee..eeeeeee.........eeeee..eeeee...............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh....eeeeee.ee..eehhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vme A  -3 HHHHmPKIWTERIFDDPEIYVLRIDDDRIRYFEAVWEIPEGISYNAYLVKLNGANVLIDGWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKTIGHDVEIIASNFGKRLLEGFYGIKDVTVVKDGEEREIGGKKFKFVmTPWLHWPDTmVTYLDGILFSCDVGGGYLLPEILDDSNESVVERYLPHVTKYIVTVIGHYKNYILEGAEKLSSLKIKALLPGHGLIWKKDPQRLLNHYVSVAKGDPKKGKVTVIYDSmYGFVENVmKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSEALIFGVSTYEAEIHPLmRFTLLEIIDKANYEKPVLVFGVHGWAPSAERTAGELLKETKFRILSFTEIKGSNmDERKIEEAISLLKKELE 398
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256      |266    |  276       286       296       306       316       326       336       346       356       366       376    |  386       396  
                                |                                                                                                                                              146-MSE   156-MSE                                                                                                    263-MSE 271-MSE                                                326-MSE                                                381-MSE             
                                1-MSE                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with Q9WZL4_THEMA | Q9WZL4 from UniProtKB/TrEMBL  Length:398

    Alignment length:400
                              1                                                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398
         Q9WZL4_THEMA     - --MPKIWTERIFDDPEIYVLRIDDDRIRYFEAVWEIPEGISYNAYLVKLNGANVLIDGWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKTIGHDVEIIASNFGKRLLEGFYGIKDVTVVKDGEEREIGGKKFKFVMTPWLHWPDTMVTYLDGILFSCDVGGGYLLPEILDDSNESVVERYLPHVTKYIVTVIGHYKNYILEGAEKLSSLKIKALLPGHGLIWKKDPQRLLNHYVSVAKGDPKKGKVTVIYDSMYGFVENVMKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSEALIFGVSTYEAEIHPLMRFTLLEIIDKANYEKPVLVFGVHGWAPSAERTAGELLKETKFRILSFTEIKGSNMDERKIEEAISLLKKELE 398
               SCOP domains --d1vmeb2 B:1-250 ROO-like flavoprotein TM0755, N-terminal domain                                                                                                                                                                                           d1vmeb1 B:251-398 ROO-like flavoprotein TM0755, C-terminal domain                                                                                    SCOP domains
               CATH domains 1vmeB01 B:-1-249 Metallo-beta-lactamase, chain A                                                                                                                                                                                                           1vmeB02 B:250-398  [code=3.40.50.360, no name defined]                                                                                                CATH domains
           Pfam domains (1) ------------------------------------Lactamase_B-1vmeB03 B:35-228                                                                                                                                                                      -----------------------------Flavodoxin_1-1vmeB01 B:258-391                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Lactamase_B-1vmeB04 B:35-228                                                                                                                                                                      -----------------------------Flavodoxin_1-1vmeB02 B:258-391                                                                                                        ------- Pfam domains (2)
         Sec.struct. author .....eeeeeee...eeeeeeeee....eehhhee....eeeeeeeeee..eeeee...hhhhhhhhhhhhhh..hhhhh.eee....hhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh...eee.....eeee..eeeeeee.........eeeee..eeeee...............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh....eeeeee.ee..eehhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vme B  -1 HHmPKIWTERIFDDPEIYVLRIDDDRIRYFEAVWEIPEGISYNAYLVKLNGANVLIDGWKGNYAKEFIDALSKIVDPKEITHIIVNHTEPDHSGSLPATLKTIGHDVEIIASNFGKRLLEGFYGIKDVTVVKDGEEREIGGKKFKFVmTPWLHWPDTmVTYLDGILFSCDVGGGYLLPEILDDSNESVVERYLPHVTKYIVTVIGHYKNYILEGAEKLSSLKIKALLPGHGLIWKKDPQRLLNHYVSVAKGDPKKGKVTVIYDSmYGFVENVmKKAIDSLKEKGFTPVVYKFSDEERPAISEILKDIPDSEALIFGVSTYEAEIHPLmRFTLLEIIDKANYEKPVLVFGVHGWAPSAERTAGELLKETKFRILSFTEIKGSNmDERKIEEAISLLKKELE 398
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    |  268  |    278       288       298       308       318       328       338       348       358       368       378  |    388       398
                              1-MSE                                                                                                                                          146-MSE   156-MSE                                                                                                    263-MSE 271-MSE                                                326-MSE                                                381-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  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Flavoprotein (71)
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WZL4_THEMA | Q9WZL4)
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:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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.
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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FEO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:12 - Pro A:13   [ RasMol ]  
    Asp B:12 - Pro B:13   [ RasMol ]  
    Leu A:150 - His A:151   [ RasMol ]  
    Leu B:150 - His B:151   [ 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
  1vme
    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
  Q9WZL4_THEMA | Q9WZL4
    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
  Q9WZL4_THEMA | Q9WZL4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9WZL4_THEMA | Q9WZL4: 4dik 4dil 5v8s

(-) Related Entries Specified in the PDB File

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