4V0S

Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.138 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M.Otero, J.M.Peon, A.van Raaij, M.J.Lamb, H.Hawkings, A.R.Gonzalez-Bello, C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASE
A, B
146Mycobacterium tuberculosisMutation(s): 1 
EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPX7 
Go to UniProtKB:  P9WPX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPX7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2HN
Query on 2HN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B]
(1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid
C14 H11 F5 O6
ZNZHQTVBMHBUCF-GLOYCNQYSA-N
7HN
Query on 7HN

Download Ideal Coordinates CCD File 
E [auth A]3,4-DIHYDROXY-2-[(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL]BENZOIC ACID
C14 H7 F5 O4
OKFLUGFRGVSRHK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.138 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.848α = 90
b = 65.187β = 90
c = 94.755γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description