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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEXAMERIC THIOESTERASE Y2039 FROM YERSINIA PESTIS
 
Authors :  C. M. D. Swarbrick, J. K. Forwood
Date :  08 Sep 15  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Thioesterase, Hot-Dog Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. D. Swarbrick, J. K. Forwood
Crystal Structure Of The Hexameric Thioesterase Y2039 From Yersinia Pestis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ACYL-COA THIOESTER HYDROLASE
    Chains: A, B, C, D, E, F
    EC Number: 3.1.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: Y2039, YPO2195
    Organism Scientific: YERSINIA PESTIS KIM10+
    Organism Taxid: 632
    Strain: KIM10+

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PGE3Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:90 , GLY A:91 , HIS A:92binding site for residue GOL A 201
2AC2SOFTWAREILE B:88 , THR B:90 , GLY B:91 , SER B:138binding site for residue PGE B 201
3AC3SOFTWAREILE C:88 , THR C:90 , PRO E:15binding site for residue PGE C 201
4AC4SOFTWAREILE D:88binding site for residue PGE D 201
5AC5SOFTWAREILE E:88 , THR E:90binding site for residue GOL E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DM5)

(-) Exons   (0, 0)

(no "Exon" information available for 5DM5)

(-) 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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee........eeeeeeeeee....eeeeeeeeee........eeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 A  13 SLPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKEPIGQRYRATEAVFTYVAVDDAGK 132
                                    22        32        42        52        62        72        82        92       102  ||   115       125       
                                                                                                                      105|                       
                                                                                                                       109                       


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..............hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeee...........eeeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 B  14 LPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKVSSEPIGQRYRATEAVFTYVAVDDAGKPRGLPS 138
                                    23        33        43        53        63        73        83        93       103       113       123       133     


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeeee.....eeeeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 C  14 LPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKVSQRYRATEAVFTYVAVDDAGKPRGLPSG 139
                                    23        33        43        53        63        73        83        93       103   ||  118       128       138 
                                                                                                                       107|                          
                                                                                                                        113                          


Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.........eeeeeeeeeee...eeeeeeeeee......eeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 D  13 SLPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKVSQRYRATEAVFTYVAVDDAGKPRGLPS 138
                                    22        32        42        52        62        72        82        92       102    || 117       127       137 
                                                                                                                        107|                         
                                                                                                                         113                         


Chain E from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeeee...eeeeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 E  14 LPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKQRYRATEAVFTYVAVDDAGKPRGLPSG 139
                                    23        33        43        53        63        73        83        93       103 ||    120       130         
                                                                                                                     105|                          
                                                                                                                      113                          


Chain F from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhh........hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee........eeeeeeeeeee...eeeeeeeeee.......eeeeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dm5 F  14 LPNGELVLRTLAMPADTNANGDIFGGWLMSQMDIGGAIQAKEIAQGRVVTVRVDGMTFLKPVAVGDVVCCYARCIKTGHSSITINIEVWVKKVSGQRYRATEAVFTYVAVDDAGKPRGLPSG 139
                                    23        33        43        53        63        73        83        93       103   ||  117       127       137  
                                                                                                                       107|                           
                                                                                                                        112
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  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 5DM5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DM5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DM5)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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