2BT4 | pdb_00002bt4

Type II Dehydroquinase inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb2BT4/pdb

• Classification: LYASE
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-05-26 Released: 2006-02-13 
• Deposition Author(s): Toscano, M.D., Stewart, K.A., Coggins, J.R., Lapthorn, A.J., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Rational Design of New Bifunctional Inhibitors of Type II Dehydroquinase.

Toscano, M.D., Stewart, K.A., Coggins, J.R., Lapthorn, A.J., Abell, C.

(2005) Org Biomol Chem 3: 3102

• PubMed: 16106291 
• DOI: https://doi.org/10.1039/b507156a
• Primary Citation Related Structures: 
  2BT4


• PubMed Abstract: 
  

  Selective inhibitors of type II dehydroquinase were rationally designed to explore a second binding-pocket in the active-site. The molecular modelling, synthesis, inhibition studies and crystal structure determination are described.

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Organizational Affiliation: 
• University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 206.11 kDa 
• Atom Count: 15,641 
• Modeled Residue Count: 1,788 
• Deposited Residue Count: 1,884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C, D, E, F, G, H, I, J, K, L	157	Streptomyces coelicolor	Mutation(s): 0  EC: 4.2.1.10
UniProt
Find proteins for P15474 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore P15474  Go to UniProtKB:  P15474

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA2	AA [auth F], DA [auth G], FA [auth H], IA [auth I], LA [auth J], M [auth A], NA [auth K], PA [auth L], Q [auth B], S [auth C], U [auth D], X [auth E]	(1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID C16 H22 O6 SCUFESRLGCQXRX-DCDXPUDHSA-N
TRS	BA [auth F], GA [auth H], O [auth A], RA [auth L]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	JA [auth I], N [auth A], QA [auth L], V [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	CA [auth F], EA [auth G], HA [auth H], KA [auth I], MA [auth J], OA [auth K], P [auth A], R [auth B], T [auth C], W [auth D], Y [auth E], Z [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.616	α = 65.91
b = 196.487	β = 65.91
c = 240.626	γ = 90.01

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-13 
Deposition Author(s): Toscano, M.D., Stewart, K.A., Coggins, J.R., Lapthorn, A.J., Abell, C.

Revision History  

• Version 1.0: 2006-02-13
  Type: Initial release
  
• Version 1.1: 2011-06-09
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description