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 ANALYSIS OF W21A MUTANT OF HUMAN GSTA1-1 IN COMPLEX WITH S-HEXYLGLUTATHIONE
 
Authors :  S. Fanucchi, I. A. Achilonu, R. J. Adamson, M. A. Fernandes, J. P. Burke,
Date :  10 Dec 09  (Deposition) - 12 Jan 10  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thioredoxin, S-Hexylglutathione, Glutathione S-Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Balchin, S. Fanucchi, I. Achilonu, R. J. Adamson, J. Burke, M. Fernandes, S. Gildenhuys, H. W. Dirr
Stability Of The Domain Interface Contributes Towards The Catalytic Function At The H-Site Of Class Alpha Glutathione Transferase A1-1.
Biochim. Biophys. Acta V. 1804 2228 2010
PubMed-ID: 20833278  |  Reference-DOI: 10.1016/J.BBAPAP.2010.09.003

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE A1
    ChainsA, B
    EC Number2.5.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKAH1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGSTA1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGTH1, HA SUBUNIT 1, GST-EPSILON, GSTA1-1, GST CLASS-ALPHA MEMBER 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GTX2Ligand/IonS-HEXYLGLUTATHIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:9 , ARG A:15 , ARG A:45 , GLN A:54 , VAL A:55 , PRO A:56 , GLN A:67 , THR A:68 , VAL A:111 , PHE A:220 , HOH A:234 , HOH A:250 , HOH A:290 , HOH A:381 , ASP B:101 , ARG B:131BINDING SITE FOR RESIDUE GTX A 5100
2AC2SOFTWAREASP A:101 , ARG A:131 , TYR B:9 , ARG B:15 , ARG B:45 , GLN B:54 , VAL B:55 , GLN B:67 , THR B:68 , LEU B:107 , MET B:208 , PHE B:220 , HOH B:247 , HOH B:313BINDING SITE FOR RESIDUE GTX B 5200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L0H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:55 -Pro A:56
2Val B:55 -Pro B:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033978T19IGSTA1_HUMANPolymorphism1051578A/BT19I
2UniProtVAR_049482P113QGSTA1_HUMANPolymorphism1051745A/BP113Q
3UniProtVAR_049483K117QGSTA1_HUMANPolymorphism1051757A/BK117Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.GSTA1_HUMAN3-83  1A:3-83
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.GSTA1_HUMAN85-207
 
  2A:85-207
B:85-207

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003345751aENSE00002201258chr6:52668708-52668583126GSTA1_HUMAN-00--
1.2ENST000003345752ENSE00002162073chr6:52664095-52663979117GSTA1_HUMAN1-29292A:2-29
B:4-29
28
26
1.3ENST000003345753ENSE00002190926chr6:52662435-5266238452GSTA1_HUMAN30-47182A:30-47
B:30-47
18
18
1.4ENST000003345754ENSE00002186617chr6:52661112-52660980133GSTA1_HUMAN47-91452A:47-91
B:47-91
45
45
1.5bENST000003345755bENSE00002141355chr6:52659064-52658923142GSTA1_HUMAN91-138482A:91-138
B:91-138
48
48
1.6ENST000003345756ENSE00002159902chr6:52657785-52657654132GSTA1_HUMAN139-182442A:139-182
B:139-182
44
44
1.7ENST000003345757ENSE00002170665chr6:52656778-52656462317GSTA1_HUMAN183-222402A:183-222
B:183-222
40
40

(-) 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:221
 aligned with GSTA1_HUMAN | P08263 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 
          GSTA1_HUMAN     2 AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
               SCOP domains d3l0ha1 A:2-80 Class alpha GST                                                 d3l0ha2 A:81-222 Class alpha GST                                                                                                               SCOP domains
               CATH domains 3l0hA01 A:2-81,A:191-222 Glutaredoxin                                           3l0hA02 A:82-190  [code=1.20.1050.10, no name defined]                                                       3l0hA01 A:2-81,A:191-222         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhhh....eeee..hhhhhhhhhhh.........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------I---------------------------------------------------------------------------------------------Q---Q--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GST_NTER  PDB: A:3-83 UniProt: 3-83                                              -GST_CTER  PDB: A:85-207 UniProt: 85-207                                                                                    --------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:2-29       Exon 1.3          -------------------------------------------Exon 1.5b  PDB: A:91-138 UniProt: 91-138        Exon 1.6  PDB: A:139-182 UniProt: 139-182   Exon 1.7  PDB: A:183-222                 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: A:47-91 UniProt: 47-91        ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3l0h A   2 AEKPKLHYFNARGRMESTRALLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with GSTA1_HUMAN | P08263 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:219
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         
          GSTA1_HUMAN     4 KPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
               SCOP domains d3l0hb1 B:4-80 Class alpha GST                                               d3l0hb2 B:81-222 Class alpha GST                                                                                                               SCOP domains
               CATH domains 3l0hB01 B:4-81,B:191-222 Glutaredoxin                                         3l0hB02 B:82-190  [code=1.20.1050.10, no name defined]                                                       3l0hB01 B:4-81,B:191-222         CATH domains
           Pfam domains (1) -GST_N-3l0hB03 B:5-77                                                     ---------------------GST_C-3l0hB01 B:99-192                                                                        ------------------------------ Pfam domains (1)
           Pfam domains (2) -GST_N-3l0hB04 B:5-77                                                     ---------------------GST_C-3l0hB02 B:99-192                                                                        ------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeee.....hhhhhhhhhhh....eeeee.hhhhhhhhhhh.........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------I---------------------------------------------------------------------------------------------Q---Q--------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GST_NTER  PDB: - UniProt: 3-83                                                  -GST_CTER  PDB: B:85-207 UniProt: 85-207                                                                                    --------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:4-29     Exon 1.3          -------------------------------------------Exon 1.5b  PDB: B:91-138 UniProt: 91-138        Exon 1.6  PDB: B:139-182 UniProt: 139-182   Exon 1.7  PDB: B:183-222                 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.4  PDB: B:47-91 UniProt: 47-91        ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3l0h B   4 KPKLHYFNARGRMESTRALLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKERALIDMYIEGIADLGEMILLLPVCPPEEKDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEEARKIFRF 222
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)
(-)
Family: GST_C (102)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GSTA1_HUMAN | P08263)
molecular function
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    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:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:1901687    glutathione derivative biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione derivative.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

 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
    GTX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:55 - Pro A:56   [ RasMol ]  
    Val B:55 - Pro B:56   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3l0h
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GSTA1_HUMAN | P08263
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.5.1.18
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GSTA1_HUMAN | P08263
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GSTA1_HUMAN | P082631gsd 1gse 1gsf 1guh 1k3l 1k3o 1k3y 1lbk 1pkw 1pkz 1pl1 1pl2 1usb 1xwg 1ydk 2r3x 2r6k 3i69 3i6a 3ik9 3ktl 3q74 3u6v 3zfb 3zfl 4hj2 5jcu 5lcz 5ld0

(-) Related Entries Specified in the PDB File

3ktl