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 :  STRUCTURE OF THE HD-DOMAIN PHOSPHOHYDROLASE OXSA
 
Authors :  J. Bridwell-Rabb, C. L. Drennan
Date :  06 Oct 16  (Deposition) - 16 Nov 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxetanocin, Hd-Domain Phosphohydrolase, Metalloprotein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bridwell-Rabb, G. Kang, A. Zhong, H. W. Liu, C. L. Drennan
An Hd Domain Phosphohydrolase Active Site Tailored For Oxetanocin-A Biosynthesis.
Proc. Natl. Acad. Sci. V. 113 13750 2016 U. S. A.
PubMed-ID: 27849620  |  Reference-DOI: 10.1073/PNAS.1613610113

(-) Compounds

Molecule 1 - OXSA PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell: E. COLI BL21 STAR (DE3)
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET24B(+)
    Gene: OXSA
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:31 , HIS A:66 , ASP A:67 , ASP A:132 , HOH A:306 , HOH A:311binding site for residue MG A 201
2AC2SOFTWARETYR A:137 , GLY A:159 , ASP A:163 , GLN A:176 , HOH A:310binding site for residue EDO A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TKA)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TKA)

(-) Exons   (0, 0)

(no "Exon" information available for 5TKA)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tka A   2 SSLLDIIYQLRQVPRWDGSFQFEKEDVSQHSFSVIAISHILCELKETLEGKKINKEKLLLYALYHDVTEVVSTHKNSLFDNLPITLSDTLSTILNNNDLEIQEIVEHADHVDAYCKSCIEVHRGNKDFISIQRSLGDKLDNLTKEYPYLKEFQNLFLKDFPLENKNY 190
                                    11        21        31        41        51        61        71   ||  103       113       123       133       143       153       163       173       183       
                                                                                                    75|                                                                                            
                                                                                                     98
   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  (0, 0)

(no "SCOP Domain" information available for 5TKA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TKA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TKA)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5TKA)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:183 - Pro A:184   [ RasMol ]  
 
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
  5tka
    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
  O24769_BACME | O24769
    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
  O24769_BACME | O24769
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O24769_BACME | O24769: 5tk6 5tk7 5tk8 5tk9

(-) Related Entries Specified in the PDB File

5tk6 SAME PROTEIN COMPLEXED WITH OXETANOCIN A DIPHOSPHATE
5tk7 SAME PROTEIN COMPLEXED WITH OXETANOCIN A TRIPHOSPHATE
5tk8 SAME PROTEIN COMPLEXED WITH OXETANOCIN A MONOPHOSPHATE
5tk9 SAME PROTEIN COMPLEXED WITH OXETANOCIN A