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 :  STRUCTURE OF PROBABLE GLUTATHIONE S-TRANSFERASE(PP0183) FROM PSEUDOMONAS PUTIDA
 
Authors :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  25 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Glutathione S-Transferase, Pp0183, Transferase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Structure Of Probable Glutathione S-Transferase(Pp0183) From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTATHIONE S-TRANSFERASE FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PP0183
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 32)

Asymmetric Unit (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LXZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Val A:49 -Pro A:50
2Ala A:143 -Pro A:144
3Val B:49 -Pro B:50
4Ala B:143 -Pro B:144
5Val C:49 -Pro C:50
6Ala C:143 -Pro C:144
7Val D:49 -Pro D:50
8Ala D:143 -Pro D:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LXZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LXZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3LXZ)

(-) 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:218
 aligned with Q88RE7_PSEPK | Q88RE7 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         Q88RE7_PSEPK     1 MLKLYGFSVSNYYNMVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGMSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLMFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLMGENPHMPRILADKEASMPAFMEMIRSG 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxz A   1 SLKLYGFSVSNYYNmVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGmSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLmFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLmGENPHmPRILADKEASmPAFmEmIRSG 218
                                    10    |   20        30        40        50        60        70        80        90       100       110    |  120       130       140       150      |160       170       180       190|     |200       210 | |    
                                         15-MSE                                                                                             115-MSE                                   157-MSE                           191-MSE |        208-MSE |    
                                                                                                                                                                                                                              197-MSE        212-MSE  
                                                                                                                                                                                                                                               214-MSE


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q88RE7_PSEPK | Q88RE7 from UniProtKB/TrEMBL  Length:220

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         Q88RE7_PSEPK     1 MLKLYGFSVSNYYNMVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGMSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLMFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLMGENPHMPRILADKEASMPAFMEMIRS 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxz B   1 SLKLYGFSVSNYYNmVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGmSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLmFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLmGENPHmPRILADKEASmPAFmEmIRS 217
                                    10    |   20        30        40        50        60        70        80        90       100       110    |  120       130       140       150      |160       170       180       190|     |200       210 | |   
                                         15-MSE                                                                                             115-MSE                                   157-MSE                           191-MSE |        208-MSE |   
                                                                                                                                                                                                                              197-MSE        212-MSE 
                                                                                                                                                                                                                                               214-MSE


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with Q88RE7_PSEPK | Q88RE7 from UniProtKB/TrEMBL  Length:220

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         Q88RE7_PSEPK     1 MLKLYGFSVSNYYNMVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGMSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLMFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLMGENPHMPRILADKEASMPAFMEMIRSG 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhh....eeee.....hhhhhhhh......eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxz C   1 SLKLYGFSVSNYYNmVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGmSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLmFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLmGENPHmPRILADKEASmPAFmEmIRSG 218
                                    10    |   20        30        40        50        60        70        80        90       100       110    |  120       130       140       150      |160       170       180       190|     |200       210 | |    
                                         15-MSE                                                                                             115-MSE                                   157-MSE                           191-MSE |        208-MSE |    
                                                                                                                                                                                                                              197-MSE        212-MSE  
                                                                                                                                                                                                                                               214-MSE


Chain D from PDB  Type:PROTEIN  Length:217
 aligned with Q88RE7_PSEPK | Q88RE7 from UniProtKB/TrEMBL  Length:220

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         Q88RE7_PSEPK     1 MLKLYGFSVSNYYNMVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGMSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLMFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLMGENPHMPRILADKEASMPAFMEMIRS 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---GST_N_3-3lxzD05 D:4-77                                                    -------------------------GST_C-3lxzD01 D:103-195                                                                      ---------------------- Pfam domains (1)
           Pfam domains (2) ---GST_N_3-3lxzD06 D:4-77                                                    -------------------------GST_C-3lxzD02 D:103-195                                                                      ---------------------- Pfam domains (2)
           Pfam domains (3) ---GST_N_3-3lxzD07 D:4-77                                                    -------------------------GST_C-3lxzD03 D:103-195                                                                      ---------------------- Pfam domains (3)
           Pfam domains (4) ---GST_N_3-3lxzD08 D:4-77                                                    -------------------------GST_C-3lxzD04 D:103-195                                                                      ---------------------- Pfam domains (4)
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh...eeeee.....hhhhhh........eeee..eeeehhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxz D   1 SLKLYGFSVSNYYNmVKLALLEKGLTFEEVTFYGGQAPQALEVSPRGKVPVLETEHGFLSETSVILDYIEQTQGGKALLPADPFGQAKVRELLKEIELYIELPARTCYAESFFGmSVEPLIKEKARADLLAGFATLKRNGRFAPYVAGEQLTLADLmFCFSVDLANAVGKKVLNIDFLADFPQAKALLQLmGENPHmPRILADKEASmPAFmEmIRS 217
                                    10    |   20        30        40        50        60        70        80        90       100       110    |  120       130       140       150      |160       170       180       190|     |200       210 | |   
                                         15-MSE                                                                                             115-MSE                                   157-MSE                           191-MSE |        208-MSE |   
                                                                                                                                                                                                                              197-MSE        212-MSE 
                                                                                                                                                                                                                                               214-MSE
   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 3LXZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LXZ)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: GST_C (118)
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q88RE7_PSEPK | Q88RE7)
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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3lxz)
 
  Cis Peptide Bonds
    Ala A:143 - Pro A:144   [ RasMol ]  
    Ala B:143 - Pro B:144   [ RasMol ]  
    Ala C:143 - Pro C:144   [ RasMol ]  
    Ala D:143 - Pro D:144   [ RasMol ]  
    Val A:49 - Pro A:50   [ RasMol ]  
    Val B:49 - Pro B:50   [ RasMol ]  
    Val C:49 - Pro C:50   [ RasMol ]  
    Val D:49 - Pro D:50   [ 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
  3lxz
    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
  Q88RE7_PSEPK | Q88RE7
    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)
  (no 'Enzyme Classificator' available)
    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
  Q88RE7_PSEPK | Q88RE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q88RE7_PSEPK | Q88RE7: 3pr8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3LXZ)