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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT-D97N OF PEPTIDYL-TRNA HYDROLASE FROM VIBRIO CHOLERAE
 
Authors :  S. Shahid, A. Kabra, R. K. Pal, A. Arora
Date :  03 Mar 16  (Deposition) - 08 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peptidyl-Trna Hydrolase, D97N Mutant, Vibrio Cholerae, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kabra, S. Shahid, R. K. Pal, R. Yadav, S. V. Pulavarti, A. Jain, S. Tripathi, A. Arora
Unraveling The Stereochemical And Dynamic Aspects Of The Catalytic Site Of Bacterial Peptidyl-Trna Hydrolase.
Rna V. 23 202 2017
PubMed-ID: 28096445  |  Reference-DOI: 10.1261/RNA.057620.116

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A, B
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PTH, VC_2184
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961
    Synonym: PTH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
12CO2Mod. Amino AcidS-HYDROPEROXYCYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 5IKE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val B:2 -Ser B:3
2Gly B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IKE)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ike A   3 SQPIKLLVGLANPGPEYAKTRHNAGAWVVEELARIHNVTLKNEPKFFGLTGRLLINSQELRVLIPTTFMNLSGKAIAALANFYQIKPEEIMVAHNELDLPPGVAKFKQGGGHGGHNGLKDTISKLGNNKEFYRLRLGIGHPGHKDKVAGYVLGKAPAKEQEcLDAAVDESVRCLEILMKDGLTKAQNRLHTFKAE 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 |     172       182       192     
                                                                                                                                                                                           164-2CO                             


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..........hhhhhhhhhhhhhhhhh....ee.hhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ike B   2 VSQPIKLLVGLANPGPEYAKTRHNAGAWVVEELARIHNVTLKNEPKFFGLTGRLLINSQELRVLIPTTFMNLSGKAIAALANFYQIKPEEIMVAHNELDLPPGVAKFKQGGGHGGHNGLKDTISKLGNNKEFYRLRLGIGHPGHKDKVAGYVLGKAPAKEQEcLDAAVDESVRCLEILMKDGLTKAQNRLHTFKAE 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  |    171       181       191      
                                                                                                                                                                                            164-2CO
   Legend:   → Mismatch (orange background)
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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 5IKE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly B:16 - Pro B:17   [ RasMol ]  
    Val B:2 - Ser B:3   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTH_VIBCH | Q9KQ21: 4z86 4zxp 5b6j 5ekt 5imb 5ivp

(-) Related Entries Specified in the PDB File

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