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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDYL T-RNA HYDROLASE FROM PSEUDOMONAS AERUGINOSA AT 2.2 ANGSTROM RESOLUTION
 
Authors :  A. Singh, A. Kumar, A. Arora, N. Singh, M. Sinha, P. Kaur, S. Sharma, T. P.
Date :  20 Jun 12  (Deposition) - 04 Jul 12  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Singh, A. Kumar, L. Gautam, P. Sharma, M. Sinha, A. Bhushan, P. Kaur, S. Sharma, A. Arora, T. P. Singh
Structural And Binding Studies Of Peptidyl-Trna Hydrolase From Pseudomonas Aeruginosa Provide A Platform For The Structure-Based Inhibitor Design Against Peptidyl-Trna Hydrolase
Biochem. J. V. 463 329 2014
PubMed-ID: 25101795  |  Reference-DOI: 10.1042/BJ20140631

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A, B
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-NH6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTH
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: PTH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:45 , PHE A:82 , ALA B:77 , ALA B:78 , GLY B:81 , PHE B:82 , PEG B:204BINDING SITE FOR RESIDUE PEG A 201
2AC2SOFTWAREPRO A:100 , PRO A:101 , GLY A:139 , TYR A:150 , GLU A:159 , HOH A:306 , HOH A:393 , HOH A:394BINDING SITE FOR RESIDUE GOL A 202
3AC3SOFTWAREGLU A:30 , LEU A:49 , ILE A:64 , HOH A:405 , ARG B:44BINDING SITE FOR RESIDUE GOL A 203
4AC4SOFTWAREGLY B:11 , ASN B:12 , PRO B:13 , ASN B:23 , ALA B:26 , ILE B:64 , PRO B:65 , THR B:66BINDING SITE FOR RESIDUE GOL B 201
5AC5SOFTWAREGLN B:5 , LYS B:58 , ASP B:59 , HOH B:345 , HOH B:383BINDING SITE FOR RESIDUE GOL B 202
6AC6SOFTWARELEU B:97 , GLY B:113 , GLY B:114 , HIS B:140 , VAL B:147BINDING SITE FOR RESIDUE GOL B 203
7AC7SOFTWARELYS A:45 , PHE A:47 , PEG A:201 , LYS B:45 , PHE B:47 , GLN B:74 , ALA B:78BINDING SITE FOR RESIDUE PEG B 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FNO)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains d4fnoa_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhh.hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fno A   1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4fnob_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..........hhhhhhhhhhhhhhhhh...eeeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fno B   1 MTAVQLIVGLGNPGPEYDQTRHNAGALFVERLAHAQGVSLVADRKYFGLVGKFSHQGKDVRLLIPTTYMNRSGQSVAALAGFFRIAPDAILVAHDELDMPPGVAKLKTGGGHGGHNGLRDIIAQLGNQNSFHRLRLGIGHPGHSSLVSGYVLGRAPRSEQELLDTSIDFALGVLPEMLAGDWTRAMQKLHSQKA 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        PTH_PSEAE | Q9HVC3: 4dhw 4djj 4erx 4fyj 4jc4 4qaj 4qbk 4qd3

(-) Related Entries Specified in the PDB File

4erx