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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  GLUTATHIONE S-TRANSFERASE OMEGA 1 BOUND TO COVALENT INHIBITOR C4-10
 
Authors :  J. A. Stuckey
Date :  13 Mar 15  (Deposition) - 12 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Covalent Inhibitor, Thioltransferase, Chloroacetamide, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ramkumar, S. Samanta, A. Kyani, S. Yang, S. Tamura, E. Ziemke, J. A. Stuckey, S. Li, K. Chinnaswamy, H. Otake, B. Debnath, V. Yarovenko, J. S. Sebolt-Leopold, M. Ljungman, N. Neamati
Mechanistic Evaluation And Transcriptional Signature Of A Glutathione S-Transferase Omega 1 Inhibitor.
Nat Commun V. 7 13084 2016
PubMed-ID: 27703239  |  Reference-DOI: 10.1038/NCOMMS13084

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE OMEGA-1
    Chains: A, B, C
    EC Number: 2.5.1.18, 1.8.5.1, 1.20.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Gene: GSTO1, GSTTLP28
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GSTO-1,GLUTATHIONE S-TRANSFERASE OMEGA 1-1,GSTO 1-1, GLUTATHIONE-DEPENDENT DEHYDROASCORBATE REDUCTASE,MONOMETHYLARSONIC ACID REDUCTASE,MMA(V) REDUCTASE,S-(PHENACYL)GLUTATHIONE REDUCTASE, SPG-R

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
14GG3Ligand/Ion2-(ETHYLSULFANYL)-N-METHYL-N-[(1-PHENYL-1H-PYRAZOL-4-YL)METHYL]ACETAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
14GG2Ligand/Ion2-(ETHYLSULFANYL)-N-METHYL-N-[(1-PHENYL-1H-PYRAZOL-4-YL)METHYL]ACETAMIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
14GG2Ligand/Ion2-(ETHYLSULFANYL)-N-METHYL-N-[(1-PHENYL-1H-PYRAZOL-4-YL)METHYL]ACETAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:29 , PHE A:31 , CYS A:32 , PRO A:33 , PHE A:34 , LEU A:56 , ILE A:131 , ARG A:183 , TRP A:222 , PHE A:225binding site for residue 4GG A 500
2AC2SOFTWAREMET B:29 , ARG B:30 , PHE B:31 , PRO B:33 , PHE B:34 , ALA B:35 , GLU B:36 , ILE B:131 , ARG B:183 , TRP B:222 , PHE B:225 , LEU B:226 , HOH B:609binding site for Di-peptide 4GG B 500 and CYS B 32
3AC3SOFTWAREMET C:29 , ARG C:30 , PHE C:31 , PRO C:33 , PHE C:34 , ALA C:35 , GLU C:36 , LEU C:56 , ILE C:131 , ARG C:183 , TRP C:222 , PHE C:225 , HOH C:628binding site for Di-peptide 4GG C 500 and CYS C 32

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:72 -Pro A:73
2Val B:72 -Pro B:73
3Val C:72 -Pro C:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YQV)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee...hhhhhhhhhhhhhh...eeeee........hhhhhh......eeee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yqv A   5 SARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYAGLKEEFRKEFTKLEEVLTNKKTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDPTVSALLTSEKDWQGFLELYLQNSPEACDYGL 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee...hhhhhhhhhhhhhh...eeeee......hhhhhhh.......eeee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yqv B   5 SARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYAGLKEEFRKEFTKLEEVLTNKKTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDPTVSALLTSEKDWQGFLELYLQNSPEACDYGL 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       


Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee...hhhhhhhhhhhhhh....eeee......hhhhhhh.......eeee....eeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yqv C   5 SARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVININLKNKPEWFFKKNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKKLLPDDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYAGLKEEFRKEFTKLEEVLTNKKTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMAAMKEDPTVSALLTSEKDWQGFLELYLQNSPEACDYGL 241
                                    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  (0, 0)

(no "SCOP Domain" information available for 4YQV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

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
    4GG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:72 - Pro A:73   [ RasMol ]  
    Val B:72 - Pro B:73   [ RasMol ]  
    Val C:72 - Pro C:73   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4yqv
    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
  GSTO1_HUMAN | P78417
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.20.4.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.8.5.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  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
  GSTO1_HUMAN | P78417
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GSTO1_HUMAN | P78417: 1eem 3lfl 3vln 4is0 4yqm 4yqu

(-) Related Entries Specified in the PDB File

4yqm 4yqu