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 ANALYSIS OF PRECORRIN-8X METHYL MUTASE FROM THERMUS THERMOPHILUS
 
Authors :  E. Inagaki, T. H. Tahirov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Jan 04  (Deposition) - 10 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Wind, Doubly Wound Sheet, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Inagaki, T. H. Tahirov
Crystal Analysis Of Precorrin-8X Methyl Mutase From Thermus Thermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRECORRIN-8X METHYL MUTASE
    Chains: A, B
    EC Number: 5.4.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:35 , HIS A:38 , ALA A:195 , HIS A:198BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:35 , ARG A:84 , ARG A:202 , HOH A:1020BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREARG B:35 , ARG B:84 , ALA B:195 , HIS B:198 , HOH B:1032 , HOH B:1071 , HOH B:1072BINDING SITE FOR RESIDUE SO4 B 1003
4AC4SOFTWAREGLU B:9 , ARG B:35 , ARG B:84 , ARG B:202 , HOH B:1011 , HOH B:1025BINDING SITE FOR RESIDUE SO4 B 1004
5AC5SOFTWAREPHE B:163 , VAL B:164 , ASN B:165 , VAL B:166 , LEU B:167 , GLU B:168 , ARG B:186BINDING SITE FOR RESIDUE SO4 B 1005
6AC6SOFTWARELYS B:46BINDING SITE FOR RESIDUE CL B 1006

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:78 -B:78

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V9C)

(-) Exons   (0, 0)

(no "Exon" information available for 1V9C)

(-) 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:198
 aligned with P83848_THETH | P83848 from UniProtKB/TrEMBL  Length:218

    Alignment length:204
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    
         P83848_THETH     6 RAIEEESFRIVDQEAGPHGFSPLEWPVVRRMIHATADFEYKALTRFSQGAVEAGLKAIQAGARILVDARMIACGLNPERLRLFGNEVVELLAHPEVVARAKATGGTRAEAAVAYAWEKGLLDGAIVGVGNAPTFLLALVEAIRQGARPALVLGMPVGFVNVLEAKRALMEAPVPWIVTEGRKGGSTLVVAALHALIRLAADGGV 209
               SCOP domains d1v9ca_ A: Precorrin-8x methylmutase                                                                                                                                                                         SCOP domains
               CATH domains 1v9cA00 A:6-209 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhheee..hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh..eee...hhhhhhh------hhhhhhhhhhhh.......eeee......hhhhhhhhhh.....eeee......hhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v9c A   6 RAIEEESFRIVDQEAGPHGFSPLEWPVVRRMIHATADFEYKALTRFSQGAVEAGLKAIQAGARILVDARMIACGLNPERLRLFGNEVVELLAHPEVVAR------TRAEAAVAYAWEKGLLDGAIVGVGNAPTFLLALVEAIRQGARPALVLGMPVGFVNVLEAKRALMEAPVPWIVTEGRKGGSTLVVAALHALIRLAADGGV 209
                                    15        25        35        45        55        65        75        85        95        |-     | 115       125       135       145       155       165       175       185       195       205    
                                                                                                                            104    111                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with P83848_THETH | P83848 from UniProtKB/TrEMBL  Length:218

    Alignment length:208
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
         P83848_THETH     5 GRAIEEESFRIVDQEAGPHGFSPLEWPVVRRMIHATADFEYKALTRFSQGAVEAGLKAIQAGARILVDARMIACGLNPERLRLFGNEVVELLAHPEVVARAKATGGTRAEAAVAYAWEKGLLDGAIVGVGNAPTFLLALVEAIRQGARPALVLGMPVGFVNVLEAKRALMEAPVPWIVTEGRKGGSTLVVAALHALIRLAADGGVDTS 212
               SCOP domains d1v9cb_ B: Precorrin-8x methylmutase                                                                                                                                                                             SCOP domains
               CATH domains 1v9cB00 B:5-212 Precorrin-8X methylmutase CbiC/CobH                                                                                                                                                              CATH domains
           Pfam domains (1) --CbiC-1v9cB01 B:7-205                                                                                                                                                                                   ------- Pfam domains (1)
           Pfam domains (2) --CbiC-1v9cB02 B:7-205                                                                                                                                                                                   ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhheee..hhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhh--hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh......eeee......hhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9c B   5 GRAIEEESFRIVDQEAGPHGFSPLEWPVVRRMIHATADFEYKALTRFSQGAVEAGLKAIQAGARILVDARMIACGLNPERLRLFGNEVVELLAHPEVVARAKAT--TRAEAAVAYAWEKGLLDGAIVGVGNAPTFLLALVEAIRQGARPALVLGMPVGFVNVLEAKRALMEAPVPWIVTEGRKGGSTLVVAALHALIRLAADGGVDTS 212
                                    14        24        34        44        54        64        74        84        94       104   |  |114       124       134       144       154       164       174       184       194       204        
                                                                                                                                 108  |                                                                                                     
                                                                                                                                    111
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CbiC] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P83848_THETH | P83848)
molecular function
    GO:0016993    precorrin-8X methylmutase activity    Catalysis of the reaction: precorrin-8X = hydrogenobyrinate.
biological process
    GO:0009236    cobalamin biosynthetic process    The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

 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 ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v9c)
 

(-) 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
  1v9c
    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
  P83848_THETH | P83848
    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)
  5.4.1.2
    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
  P83848_THETH | P83848
    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 1V9C)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V9C)