7NNC

Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal-5'-phosphate and 6-Methoxyquinoline-3-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis

Gupta, P.Thomas, S.E.Zaidan, S.A.Pasillas, M.A.Cory-Wright, J.Sebastian-Perez, V.Burgess, A.Cattermole, E.Meghir, C.Abell, C.Coyne, A.G.Jacobs, W.R.Blundell, T.L.Tiwari, S.Mendes, V.

(2021) Comput Struct Biotechnol J 19: 3491-3506


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetylornithine aminotransferaseA, B, C, D402Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argDRv1655MTCY06H11.20
EC: 2.6.1.11
UniProt
Find proteins for P9WPZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPZ7 
Go to UniProtKB:  P9WPZ7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMH (Subject of Investigation/LOI)
Query on UMH

Download Ideal Coordinates CCD File 
F [auth D]6-methoxyquinoline-3-carboxylic acid
C11 H9 N O3
QSFFBQNKTUMKNW-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth B], G [auth D]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, DL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.461α = 90
b = 184.944β = 106.06
c = 71.578γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1158806

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release