Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

> Summary

Summary for 2NAF

DescriptorPeptidyl-tRNA hydrolase (E.C.
Functional Keywordsprotein, hydrolase
Biological sourceMycobacterium smegmatis str. MC2 155
Cellular locationCytoplasm  A0R3D3
Total number of polymer chains1
Total molecular weight20306.49
Yadav, R.,Pathak, P.,Fatma, F.,Kabra, A.,Pulavarti, S.,Jain, A.,Kumar, A.,Shukla, V.,Arora, A. (deposition date: 2015-12-23, release date: 2017-01-11)
Primary citation
Kabra, A.,Fatma, F.,Shahid, S.,Pathak, P.P.,Yadav, R.,Pulavarti, S.V.,Tripathi, S.,Jain, A.,Arora, A.
Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy.
Biochim.Biophys.Acta, 1864:1304-1314, 2016
PubMed: 27378575
DOI: 10.1016/j.bbapap.2016.06.013
MImport into Mendeley
Experimental method

Structure validation

ClashscoreRamachandran outliersSidechain outliers111.9%5.8%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all NMR structures

More Asymmetric unit images

Molmil generated image of 2naf
no rotation
Molmil generated image of 2naf
rotated about x axis by 90°
Molmil generated image of 2naf
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight20306.5
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight20306.5
*Water molecules are not included.

> Experimental details


Experimental method:SOLUTION NMR

Spectrometer IDSpectrometer makerSpectrometer modelSpectrometer typeSpectrometer field strength
1VarianINOVAVarian INOVA600
2BrukerAvanceBruker Avance700
3BrukerAvanceBruker Avance800


experiment idconditions idsolution idExperiment type
1112D 1H-15N HSQC
2123D HNCO
3123D HNCA
6123D H(CCO)NH
7123D C(CO)NH
9113D 1H-15N NOESY
10133D 1H-13C NOESY aliphatic
11133D 1H-13C NOESY aromatic
12132D 1H-13C HSQC aliphatic
13132D 1H-13C HSQC aromatic

NMR Sample

conditions idNMR sample pHNMR sample pressureNMR sample temperature


Conformers Calculated Total Number500
Conformers Submitted Total Number10

> Functional details


Functional Information from GO Data


Functional Information from PDB Data

site_idNumber of ResiduesDetails

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan