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 :  THE STRUCTURE OF MICROSOMAL GLUTATHIONE TRANSFERASE 1
 
Authors :  Q. Kuang, P. Purhonen, C. Jegerschold, R. Morgenstern, H. Hebert
Date :  20 Feb 16  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  ELECTRON CRYSTALLOGRAPHY
Resolution :  3.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane, Enzyme, Four-Helical Bundle, Trimer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Kunag, P. Purhonen, J. Alander, R. Svensson, V. Hoogland, J. Winerdal, L. Spahiu, A. Ottoson-Wadlund, C. Jegerschold, R. Morgonstern, H. Hebert
Refined Atomic Model And Insight Into The Catalytic Mechanism Of Microsomal Glutathione Transferase 1 From Electron Crystallography
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MICROSOMAL GLUTATHIONE S-TRANSFERASE 1
    Chains: A
    EC Number: 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSP19T7LT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MGST1, GST12
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: MICROSOMAL GST-1,MICROSOMAL GST-I

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2PC12Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PLM2Ligand/IonPALMITIC ACID
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1GSH3Ligand/IonGLUTATHIONE
2PC16Ligand/Ion1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3PLM6Ligand/IonPALMITIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:38 , HIS A:76 , LEU A:77binding site for residue GSH A 201
2AC2SOFTWAREILE A:105 , VAL A:136 , VAL A:140 , MET A:144binding site for residue PC1 A 202
3AC3SOFTWARETYR A:116 , ALA A:120 , PRO A:124binding site for residue PC1 A 203
4AC4SOFTWARELEU A:30 , ILE A:115 , THR A:118 , ILE A:119 , TYR A:121 , LEU A:122binding site for residue PLM A 204
5AC5SOFTWAREPRO A:85 , ILE A:89 , LEU A:92 , TYR A:93 , LEU A:149 , LEU A:153binding site for residue PLM A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I9K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:127 -Pro A:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I9K)

(-) Exons   (0, 0)

(no "Exon" information available for 5I9K)

(-) 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i9k A  10 NEVLMAFTSYATIILAKMMFLSSATAFQRLTNKDEKVERVRRAHLNDLENIVPFLGIGLLYSLSGPDLSTALIHFRIFVGARIYHTIAYLTPLPQPNRGLAFFVGYGVTLSMAYRLLRSRLYL 155
                                    19        29        39  ||    72        82        92       102       112       122       132       142       152   
                                                           42|                                                                                         
                                                            66
   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 5I9K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I9K)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5I9K)

 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
    GSH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PC1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLM  [ 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
    Gln A:127 - Pro A:128   [ 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
  5i9k
    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
  MGST1_RAT | P08011
    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)
  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
  MGST1_RAT | P08011
    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
        MGST1_RAT | P08011: 2h8a 5ia9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I9K)