5ZHK

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of TrmD from Mycobacterium tuberculosis in complex with active-site inhibitor

Zhong, W.Pasunooti, K.K.Balamkundu, S.Wong, Y.W.Nah, Q.Liu, C.F.Lescar, J.Dedon, P.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine-N(1)-)-methyltransferase
A
238Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: trmD
EC: 2.1.1.228
Find proteins for P9WFY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFY7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9D6
Query on 9D6

Download SDF File 
Download CCD File 
A
N-[(4-{[cyclohexyl(ethyl)amino]methyl}phenyl)methyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
C23 H28 N4 O2 S
VDWQEXVBMIBDPI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.090α = 90.00
b = 50.800β = 90.56
c = 58.081γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Singapore SMART Innovation CentreSingaporeING137070-BIO

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release