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(-) Description

Title :  CRYSTAL STRUCTURE OF ACINETOBACTER BAUMANNII PEPTIDYL-TRNA HYDROLASE
 
Authors :  S. Yamini, S. Kaushik, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Date :  29 Mar 13  (Deposition) - 17 Apr 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidyl-Trna Hydrolase, Enzyme, Molecular Conformation, Inhibition, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kaushik, N. Singh, S. Yamini, A. Singh, M. Sinha, A. Arora, P. Kaur, S. Sharma, T. P. Singh
The Mode Of Inhibitor Binding To Peptidyl-Trna Hydrolase: Binding Studies And Structure Determination Of Unbound And Bound Peptidyl-Trna Hydrolase From Acinetobacter Baumannii
Plos One V. 8 67547 2013
PubMed-ID: 23844024  |  Reference-DOI: 10.1371/JOURNAL.PONE.0067547

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector: PET 28A
    Expression System Vector Type: PLASMID
    Gene: HMPREF0010_01329, PTH
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 575584
    Strain: ATCC19606
    Synonym: PTH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:13 , GLY A:14 , GLU A:30 , MET A:66 , HOH A:321 , HOH A:358 , HOH A:471BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWARELYS A:45 , PRO A:78 , HOH A:494 , HOH A:500BINDING SITE FOR RESIDUE EDO A 202
3AC3SOFTWAREASP A:43 , PRO A:44 , GLY A:48BINDING SITE FOR RESIDUE EDO A 203
4AC4SOFTWARELYS A:107 , GLY A:111 , HIS A:112 , ARG A:131 , ARG A:133 , HOH A:385 , HOH A:400BINDING SITE FOR RESIDUE ACT A 204
5AC5SOFTWARETYR A:36 , ASN A:54 , GLU A:56 , TYR A:83 , GLN A:84 , HOH A:401 , HOH A:427BINDING SITE FOR RESIDUE PEG A 205
6AC6SOFTWAREGLU A:16 , TYR A:17 , SER A:146 , LEU A:150 , HOH A:443BINDING SITE FOR RESIDUE GOL A 206
7AC7SOFTWARETYR A:36 , GLY A:37 , ILE A:38 , THR A:39 , ARG A:52 , GLY A:53 , ASN A:54 , PRO A:127 , HOH A:344 , HOH A:401 , HOH A:487 , HOH A:490BINDING SITE FOR RESIDUE PEG A 207
8AC8SOFTWAREPRO A:13 , ASN A:70 , ARG A:71 , HOH A:341 , HOH A:396 , HOH A:429BINDING SITE FOR RESIDUE GOL A 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JY7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JY7)

(-) Exons   (0, 0)

(no "Exon" information available for 4JY7)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains d4jy7a_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhhh...eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee........hhhhhhhhhh...eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jy7 A   1 MSNISLIVGLGNPGSEYAQTRHNAGFWFVEQLADKYGITLKNDPKFHGISGRGNIEGHDVRLLLPMTYMNRSGQSVVPFSKFYQIAPEAILIAHDELDMNPGVIRLKTGGGHGGHNGLRDIVPHIGPNFHRLRIGIGHPGSKERVSGHVLGKAPSNEQSLMDGAIDHALSKVKLLVQGQVPQAMNQINAYKPA 193
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JY7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        D0C9L6_ACIB2 | D0C9L6: 3wh4 4fop 4fot 4hoy 4iko 4jwk 4jx9 4lwq 4lwr 4olj

(-) Related Entries Specified in the PDB File

2pth