Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF BOMBYX MORI GLUTATHIONE TRANSFERASE BMGSTD1
 
Authors :  X. Tan, X. X. Ma, X. M. Hu, Q. M. Chen, P. Zhao, Q. Y. Xia, C. Z. Zhou
Date :  20 Mar 12  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Trx-Like Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Tan, X. X. Ma, X. M. Hu, Q. M. Chen, P. Zhao, Q. Y. Xia, C. Z. Zhou
Structural Characterization Of Bombyx Mori Glutathione Transferase Bmgstd1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: SILK MOTH
    Organism Scientific: BOMBYX MORI
    Organism Taxid: 7091

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4E8E)

(-) Sites  (0, 0)

(no "Site" information available for 4E8E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E8E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:57 -Pro A:58
2Ile B:57 -Pro B:58
3Ile C:57 -Pro C:58
4Ile D:57 -Pro D:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E8E)

(-) Exons   (0, 0)

(no "Exon" information available for 4E8E)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d4e8ea1 A:0-89 automated matches                                                          d4e8ea2 A:90-215 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh...eeeee.hhhhh...hhhhhhhh......eeee..eeeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e8e A   0 HMPVQPIKLYYLPPSPPCRAVMMTARVLELDLHLITTNIMNGEHMTPEYLKMNPQHTIPTMDDNGFILWESRAIQTYLVNAYGKDDSLYPKNPRQRAIIDQRLNFDLGTLYLRYLNLYTPILFRGEAYDQEKADKFDEALGWLNTFLDGRPFVAGENMTVADITIVVTITNIDAFGYDFSSHENIAKWFERTKKMLEPYGYDEIDVTGAKMLASFL 215
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4e8eb1 B:0-89 automated matches                                                          d4e8eb2 B:90-215 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee...hhhhhhhhhhhhhh....eeee.........hhhhhhhh......eeee..eeeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e8e B   0 HMPVQPIKLYYLPPSPPCRAVMMTARVLELDLHLITTNIMNGEHMTPEYLKMNPQHTIPTMDDNGFILWESRAIQTYLVNAYGKDDSLYPKNPRQRAIIDQRLNFDLGTLYLRYLNLYTPILFRGEAYDQEKADKFDEALGWLNTFLDGRPFVAGENMTVADITIVVTITNIDAFGYDFSSHENIAKWFERTKKMLEPYGYDEIDVTGAKMLASFL 215
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      


Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4e8ec1 C:0-89 automated matches                                                          d4e8ec2 C:90-215 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh...eeeee.........hhhhhhhh......eeee..eeeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e8e C   0 HMPVQPIKLYYLPPSPPCRAVMMTARVLELDLHLITTNIMNGEHMTPEYLKMNPQHTIPTMDDNGFILWESRAIQTYLVNAYGKDDSLYPKNPRQRAIIDQRLNFDLGTLYLRYLNLYTPILFRGEAYDQEKADKFDEALGWLNTFLDGRPFVAGENMTVADITIVVTITNIDAFGYDFSSHENIAKWFERTKKMLEPYGYDEIDVTGAKMLASFL 215
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      


Chain D from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d4e8ed1 D:0-89 automated matches                                                          d4e8ed2 D:90-215 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh...eeeee.........hhhhhhhh......eeee..eeeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e8e D   0 HMPVQPIKLYYLPPSPPCRAVMMTARVLELDLHLITTNIMNGEHMTPEYLKMNPQHTIPTMDDNGFILWESRAIQTYLVNAYGKDDSLYPKNPRQRAIIDQRLNFDLGTLYLRYLNLYTPILFRGEAYDQEKADKFDEALGWLNTFLDGRPFVAGENMTVADITIVVTITNIDAFGYDFSSHENIAKWFERTKKMLEPYGYDEIDVTGAKMLASFL 215
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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, 8)

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 4E8E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E8E)

(-) Gene Ontology  (1, 1)

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
(no "Ligands, Modified Residues, Ions" information available for 4e8e)
 
  Sites
(no "Sites" information available for 4e8e)
 
  Cis Peptide Bonds
    Ile A:57 - Pro A:58   [ RasMol ]  
    Ile B:57 - Pro B:58   [ RasMol ]  
    Ile C:57 - Pro C:58   [ RasMol ]  
    Ile D:57 - Pro D:58   [ 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 | Biol. Unit 1 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
  4e8e
    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
  O61996_BOMMO | O61996
    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)
  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
  O61996_BOMMO | O61996
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O61996_BOMMO | O61996: 4e8h

(-) Related Entries Specified in the PDB File

4e8h