4CKY

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative

• PDB DOI:  https://doi.org/10.2210/pdb4CKY/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-01-10 Released: 2015-03-25 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.144 
• R-Value Work: 0.103 
• R-Value Observed: 0.105 

Literature

Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase

Maneiro, M., Otero, J.M., Peon, A., Sedes, A., Llamas-Saiz, A.L., Lamb, H., Hawkins, A.R., van Raaij, M.J., Gonzalez-Bello, C.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 16.06 kDa 
• Atom Count: 1,207 
• Modelled Residue Count: 134 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	146	Mycobacterium tuberculosis	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7  Go to UniProtKB:  P9WPX7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ND3	F [auth A]	2,2-dimethyl-3-dehydroquinic acid C9 H14 O6 FWOMLGVRVSLROK-YZNMAWMESA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	B [auth A], C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.144 
• R-Value Work: 0.103 
• R-Value Observed: 0.105 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.95	α = 90
b = 126.95	β = 90
c = 126.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Sedes, A., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references, Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references