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 OF A TAU CLASS GST MUTANT FROM GLYCINE
 
Authors :  I. Axarli, A. W. Muleta, D. Vlachakis, S. Kossida, G. Kotzia, P. Dhavala A. C. Papageorgiou, N. E. Labrou
Date :  04 Feb 15  (Deposition) - 16 Dec 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Binding Site, Catalytic Domain, Enzyme, Induction, Detoxification, Herbicides, Kinetics, Site-Directed Mutagenesis, Soy Beans, Glutathione Transferase, Protein Stability, Catalytic Mechanism, Xenobiotic Binding, Allosterism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Axarli, A. W. Muleta, D. Vlachakis, S. Kossida, G. Kotzia, A. Maltezos, P. Dhavala, A. C. Papageorgiou, N. E. Labrou
Directed Evolution Of Tau Class Glutathione Transferases Reveals A Site That Regulates Catalytic Efficiency And Masks Cooperativity.
Biochem. J. V. 473 559 2016
PubMed-ID: 26637269  |  Reference-DOI: 10.1042/BJ20150930

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: SOYBEAN
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Synonym: GMGSTU4-MUTANT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
14NM3Ligand/Ion4-NITROPHENYL METHANETHIOL
2GTB2Ligand/IonS-(P-NITROBENZYL)GLUTATHIONE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:11 , ARG A:20 , TYR A:32 , LYS A:197 , SER A:198 , LEU A:199 , PRO A:200 , SER B:177BINDING SITE FOR RESIDUE 4NM A1220
2AC2SOFTWARETYR A:107 , ARG A:111 , CYS A:114 , THR A:115 , TRP A:163 , ILE A:209 , LEU A:212 , GTB A:1222BINDING SITE FOR RESIDUE 4NM A1221
3AC3SOFTWARESER A:13 , PHE A:15 , LYS A:40 , LYS A:53 , ILE A:54 , PRO A:55 , GLU A:66 , SER A:67 , TYR A:107 , PHE A:208 , LEU A:212 , 4NM A:1221 , PO4 A:1223 , HOH A:2018 , HOH A:2056 , HOH A:2081 , HOH A:2143 , HOH A:2237 , HOH A:2238 , HOH A:2239 , LYS B:104BINDING SITE FOR RESIDUE GTB A1222
4AC4SOFTWARESER B:13 , PHE B:15 , LEU B:37 , LYS B:40 , LYS B:53 , ILE B:54 , PRO B:55 , GLU B:66 , SER B:67 , TYR B:107 , PHE B:208 , LEU B:212 , PO4 B:1222 , HOH B:2017 , HOH B:2066 , HOH B:2105 , HOH B:2169 , HOH B:2170BINDING SITE FOR RESIDUE GTB B1220
5AC5SOFTWARETYR B:107 , ARG B:111 , CYS B:114 , THR B:115 , TRP B:163 , ILE B:209 , LEU B:212BINDING SITE FOR RESIDUE 4NM B1221
6AC6SOFTWAREHIS A:51 , LYS A:53 , GLU A:66 , GTB A:1222 , LYS B:104BINDING SITE FOR RESIDUE PO4 A1223
7AC7SOFTWARELYS A:104 , LYS B:53 , GLU B:66 , GTB B:1220BINDING SITE FOR RESIDUE PO4 B1222

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:54 -Pro A:55
2Ile B:54 -Pro B:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AGY)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhh....eeee......hhhhhhhh.......eeee..eeeehhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agy A   1 MQDEVVLLDFWPSPFGMRVRIALAEKGIKYEYKEEDLQNKSPLLLKMNPVHKKIPVLIHNGKPICESLIAVQYIEEVWNDRNPLLPSDPYQRAQTRFWADYVDKKIYDLGRKICTSKGEEKEAAKKEFIEALKLLEEQLGDKTYFGGDNLGFVDIALVPFYTWFKAYETFGTLNIESECPKFVAWAKRCLQKESVAKSLPDQQKVYEFIMDLRKKLGIE 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhh...eeee......hhhhhhhh.......eeee..eeeehhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5agy B   3 DEVVLLDFWPSPFGMRVRIALAEKGIKYEYKEEDLQNKSPLLLKMNPVHKKIPVLIHNGKPICESLIAVQYIEEVWNDRNPLLPSDPYQRAQTRFWADYVDKKIYDLGRKICTSKGEEKEAAKKEFIEALKLLEEQLGDKTYFGGDNLGFVDIALVPFYTWFKAYETFGTLNIESECPKFVAWAKRCLQKESVAKSLPDQQKVYEFIMDLRKKLGIE 219
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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 5AGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    4NM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:54 - Pro A:55   [ RasMol ]  
    Ile B:54 - Pro B:55   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  5agy
    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
  I1MJ34_SOYBN | I1MJ34
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  O49235_SOYBN | O49235
    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
  I1MJ34_SOYBN | I1MJ34
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  O49235_SOYBN | O49235
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O49235_SOYBN | O49235: 2vo4 4top

(-) Related Entries Specified in the PDB File

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