7NNY

Crystal structure of Mycobacterium tuberculosis ArgF in complex with naphthalen-1-ol.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine carbamoyltransferase
A, B, C, D, E
A, B, C, D, E, F
309Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argFRv1656MTCY06H11.21
EC: 2.1.3.3
UniProt
Find proteins for P9WIT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIT9 
Go to UniProtKB:  P9WIT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1NP (Subject of Investigation/LOI)
Query on 1NP

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
CA [auth F]
I [auth A]
J [auth A]
AA [auth E],
BA [auth F],
CA [auth F],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D],
Z [auth E]
1-NAPHTHOL
C10 H8 O
KJCVRFUGPWSIIH-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth A]
M [auth B]
O [auth C]
G [auth A],
H [auth A],
L [auth A],
M [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
W [auth E],
X [auth E],
Y [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.947α = 90
b = 143.785β = 117.6
c = 97.278γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description