4CNP

Structure of the Salmonella typhi type I dehydroquinase inhibited by a 3-epiquinic acid derivative

• PDB DOI: https://doi.org/10.2210/pdb4CNP/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-23 Released: 2015-02-18 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Lence, E., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.160 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 

Starting Model: experimental

Literature

Mechanistic Insight Into the Reaction Catalyzed by Type I Dehydroquinase

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.97 kDa 
• Atom Count: 4,901 
• Modelled Residue Count: 504 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B	252	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi) Explore P24670  Go to UniProtKB:  P24670

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9C4	C [auth A], H [auth B]	(2S)-2-HYDROXY-3-EPIQUINIC ACID C7 H12 O7 OLBQNCISLUABGO-LNHNIDQWSA-N
CL	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.160 
• R-Value Work: 0.133 
• R-Value Observed: 0.134 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.216	α = 90
b = 44.473	β = 95.2
c = 84.702	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: 2015-02-18 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Maneiro, M., Peon, A., Lence, E., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description