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 MOLYBDOPTERIN CONVERTING FACTOR SUBUNIT 2 (AQ_2181) FROM AQUIFEX AEOLICUS VF5
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, Y. Agari, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)
Date :  22 Jan 07  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Moae, Coenzyme Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, Y. Agari A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Molybdopterin Converting Factor Subuni 2 (Aq_2181) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDOPTERIN-CONVERTING FACTOR SUBUNIT 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D
    Expression System Strain: BL-21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: MPT SYNTHASE SUBUNIT 2, MOLYBDOPTERIN SYNTHASE SUBUNIT 2, MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN E, MOLYBDOPTERIN-CONVERTING FACTOR LARGE SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FMT2Ligand/IonFORMIC ACID
3GOL2Ligand/IonGLYCEROL
4NA2Ligand/IonSODIUM ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:15 , GLY A:17 , ALA A:18 , HOH A:823BINDING SITE FOR RESIDUE NA A 701
2AC2SOFTWARETYR A:59 , GLU A:61 , MET A:62 , LYS B:131BINDING SITE FOR RESIDUE CL A 800
3AC3SOFTWARETRP B:15 , GLY B:17 , ALA B:18 , HOH B:837BINDING SITE FOR RESIDUE NA B 702
4AC4SOFTWAREILE A:40 , TYR A:56 , LYS A:123 , LYS A:130 , HOH A:817 , HOH A:901 , HOH A:947BINDING SITE FOR RESIDUE TRS A 603
5AC5SOFTWAREHIS A:107 , ARG A:108 , HOH A:951BINDING SITE FOR RESIDUE FMT A 604
6AC6SOFTWAREGLU B:2 , VAL B:9 , TYR B:10 , LEU B:11 , ILE B:64BINDING SITE FOR RESIDUE GOL B 601
7AC7SOFTWAREHIS B:87 , LYS B:123 , ILE B:128 , LYS B:130 , HOH B:819 , HOH B:880 , HOH B:881BINDING SITE FOR RESIDUE GOL B 602
8AC8SOFTWAREHIS B:107 , ARG B:108 , HOH B:882BINDING SITE FOR RESIDUE FMT B 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OMD)

(-) 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:135
 aligned with MOAE_AQUAE | O67928 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
           MOAE_AQUAE     1 MEVGMIPRVYLGHEWFGAERILSEYQVPEDCGAQVLFLGIPRNAPEDGGNIEALEYEAYPEMAIKEMEKIRQETIEKFGVKEVFIHHRLGLVKIGEPSFLVLAVGGHREETFKACRYAVDETKKRVPIWKKEIFK 135
               SCOP domains d2omda_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....hhhhhhhhh.......eeeeeee....hhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee.eeee.....eeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2omd A   1 MEVGMIPRVYLGHEWFGAERILSEYQVPEDCGAQVLFLGIPRNAPEDGGNIEALEYEAYPEMAIKEMEKIRQETIEKFGVKEVFIHHRLGLVKIGEPSFLVLAVGGHREETFKACRYAVDETKKRVPIWKKEIFK 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with MOAE_AQUAE | O67928 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
           MOAE_AQUAE     1 MEVGMIPRVYLGHEWFGAERILSEYQVPEDCGAQVLFLGIPRNAPEDGGNIEALEYEAYPEMAIKEMEKIRQETIEKFGVKEVFIHHRLGLVKIGEPSFLVLAVGGHREETFKACRYAVDETKKRVPIWKKEIFKEGKGEWVLGE 145
               SCOP domains d2omdb_ B: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------MoaE-2omdB01 B:8-126                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) -------MoaE-2omdB02 B:8-126                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author ........eeee....hhhhhhhhh.......eeeeeee....hhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeeee.eeee.....eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2omd B   1 MEVGMIPRVYLGHEWFGAERILSEYQVPEDCGAQVLFLGIPRNAPEDGGNIEALEYEAYPEMAIKEMEKIRQETIEKFGVKEVFIHHRLGLVKIGEPSFLVLAVGGHREETFKACRYAVDETKKRVPIWKKEIFKEGKGEWVLGE 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OMD)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MoaE] (7)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MOAE_AQUAE | O67928)
molecular function
    GO:0030366    molybdopterin synthase activity    Catalysis of the conversion of precursor Z to molybdopterin, the final step in molybdopterin biosynthesis.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
    GO:0032324    molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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 ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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
(no "Cis Peptide Bonds" information available for 2omd)
 

(-) 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
  2omd
    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
  MOAE_AQUAE | O67928
    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)
  (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
  MOAE_AQUAE | O67928
    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 2OMD)

(-) Related Entries Specified in the PDB File

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