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 :  CRYSTAL STRUCTURE OF GLUTATHIONE TRANSFERASE BGRAMDRAFT_1843 FROM BURKHOLDERIA GRAMINIS, TARGET EFI-507289, WITH TWO GLUTATHIONE MOLECULES BOUND PER ONE PROTEIN SUBUNIT
 
Authors :  Y. Patskovsky, M. W. Vetting, R. Toro, R. Bhosle, N. Al Obaidi, L. L. Mor S. R. Wasserman, S. Sojitra, M. Stead, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seide H. J. Imker, J. A. Gerlt, R. N. Armstrong, S. C. Almo, Enzyme Function Initiative (Efi)
Date :  27 Aug 13  (Deposition) - 04 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glutathione S-Transferase, Enzyme Function Initiative, Efi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, M. W. Vetting, R. Toro, R. Bhosle, N. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, M. Stead, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, R. N. Armstrong, S. C. Alm
Crystal Structure Of Glutathione Transferase Bgramdraft_184 From Burkholderia Graminis, Target Efi-507289, With Two Glutathione Molecules Bound Per One Protein Subunit
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE DOMAIN
    Chains: A
    EC Number: 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BGRAMDRAFT_1843
    Organism Scientific: BURKHOLDERIA GRAMINIS
    Organism Taxid: 396598
    Strain: C4D1M

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID
2GSH2Ligand/IonGLUTATHIONE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2GSH4Ligand/IonGLUTATHIONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:28 , ASN A:30 , PHE A:52 , GLN A:57 , ASN A:69 , LYS A:70 , ILE A:71 , PRO A:72 , GLU A:89 , SER A:90 , MET A:123 , GSH A:302 , HOH A:406 , HOH A:407 , HOH A:416 , HOH A:447 , HOH A:578 , HOH A:782BINDING SITE FOR RESIDUE GSH A 301
2AC2SOFTWAREASN A:30 , GLY A:127 , PRO A:128 , GLY A:131 , ARG A:152 , TRP A:189 , GSH A:301 , BEZ A:303 , HOH A:401 , HOH A:406 , HOH A:421 , HOH A:470 , HOH A:496 , HOH A:524 , HOH A:579 , HOH A:643BINDING SITE FOR RESIDUE GSH A 302
3AC3SOFTWARETYR A:-3 , PHE A:139 , ASN A:192 , TYR A:197 , GSH A:302 , HOH A:571 , HOH A:774BINDING SITE FOR RESIDUE BEZ A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MF6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:71 -Pro A:72
2Ser A:230 -Pro A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MF6)

(-) Exons   (0, 0)

(no "Exon" information available for 4MF6)

(-) 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:240
                                                                                                                                                                                                                                                                                
               SCOP domains d4mf6a1 A:-5-103 automated matches                                                                           d4mf6a2 A:104-234 automated matches                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhh.......eeeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh........eeee..hhhhh.eeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mf6 A  -5 NLYFQSMTDLSAFPITKKWPAAHPERLQLYSLPTPNGVKVSIMLEETGLPYEPHLVRFDTNDQLTPEFMSLNPNNKIPAIIDPNGPDGKPLPLFESGAILIYLADKTGQLIPQDAAGRYEAIQWVMFQMGGIGPMFGQLGFFHKFAGKEYEDKRPRDRYVAESKRLLGVLEQRLEGREWILGDQYSIADIATFPWVRNLIGFYEAGELVAIQDFPNVQRALAAFVARPAVVRGLDSPKRG 234
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MF6)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

 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
    BEZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:71 - Pro A:72   [ RasMol ]  
    Ser A:230 - Pro A:231   [ 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
  4mf6
    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
  B1FXZ2_9BURK | B1FXZ2
    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)
  2.5.1.18
    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
  B1FXZ2_9BURK | B1FXZ2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B1FXZ2_9BURK | B1FXZ2: 4mf5

(-) Related Entries Specified in the PDB File

4mf5 ESSENTIALLY UNLIGANDED GLUTATHIONE TRANSFERASE BGRAMDRAFT_ 1843 RELATED ID: EFI-507289 RELATED DB: TARGETTRACK