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 MONOMERIC NA-GST-3, A GLUTATHIONE S-TRANSFERASE FROM THE MAJOR HUMAN HOOKWORM PARASITE NECATOR AMERICANUS
 
Authors :  O. A. Asojo
Date :  21 Mar 13  (Deposition) - 14 Aug 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gst, Detoxification, Gsh, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kelleher, B. Zhan, O. A. Asojo
Structure Of Monomeric Na-Gst-3, A Glutathione S-Transferas From The Major Human Hookworm Parasite Necator Americanus.
Acta Crystallogr. , Sect. F V. 69 839 2013
PubMed-ID: 23908024  |  Reference-DOI: 10.1107/S1744309113017661

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE-3
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Gene: GST-3
    Organism Common: HUMAN HOOKWORM
    Organism Scientific: NECATOR AMERICANUS
    Organism Taxid: 51031

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2GSH1Ligand/IonGLUTATHIONE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2GSH2Ligand/IonGLUTATHIONE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:8 , PHE A:9 , TRP A:39 , LYS A:43 , GLN A:50 , LEU A:51 , PRO A:52 , GLN A:63 , SER A:64 , ASP A:97 , HOH A:497 , HOH A:511 , HOH A:526 , HOH A:547BINDING SITE FOR RESIDUE GSH A 301
2AC2SOFTWAREGLU A:166 , LYS A:169 , ILE A:198 , ARG A:201 , HOH A:425 , HOH A:450 , HOH A:510 , HOH A:553BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASP A:10 , ARG A:33 , SER A:35 , ARG A:129 , THR A:173 , HOH A:472 , HOH A:481 , HOH A:489BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREPRO A:47 , PHE A:135 , ASN A:138 , PHE A:139 , GLU A:142BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWAREPHE A:9 , HIS A:36BINDING SITE FOR RESIDUE GOL A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W8S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:51 -Pro A:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W8S)

(-) Exons   (0, 0)

(no "Exon" information available for 3W8S)

(-) 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:205
 aligned with D3U1A7_NECAM | D3U1A7 from UniProtKB/TrEMBL  Length:206

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
         D3U1A7_NECAM     2 VHYKLTYFDGRGAAEIIRQIFVLAGQEYEDIRLSHDEWPKYKNEMPFGQLPVLEVDGKKLAQSFAIARFVAKKFGFAGKCPFEEALVDSITDQYKDFINEIRPFLRVAMGFAEGDLEKLSNEVFLPAREKFFGFMTNFLKESKSGYLVGDSLTFADLYLAECASEFAKKTPTIFDGFPEIKAHAEKVRSNPALKKWIETRPETKF 206
               SCOP domains d3w8sa1 A:2-77 automated matches                                            d3w8sa2 A:78-206 automated matches                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhh......eeee..eeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w8s A   2 VHYKLTYFDGRGAAEIIRQIFVLAGQEYEDIRLSHDEWPKYKNEMPFGQLPVLEVDGKKLAQSFAIARFVAKKFGFAGKCPFEEALVDSITDQYKDFINEIRPFLRVAMGFAEGDLEKLSNEVFLPAREKFFGFMTNFLKESKSGYLVGDSLTFADLYLAECASEFAKKTPTIFDGFPEIKAHAEKVRSNPALKKWIETRPETKF 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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 3W8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W8S)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (D3U1A7_NECAM | D3U1A7)
molecular function
    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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSH  [ 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 ]
 
  Cis Peptide Bonds
    Leu A:51 - Pro A:52   [ 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
  3w8s
    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
  D3U1A7_NECAM | D3U1A7
    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
  D3U1A7_NECAM | D3U1A7
    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 3W8S)

(-) Related Entries Specified in the PDB File

1tw9 2on5 2on7