2Q85 | pdb_00002q85

Crystal Structure of E. Coli Mur B bound to a Naphthyl Tetronic Acid inihibitor

• PDB DOI: https://doi.org/10.2210/pdb2Q85/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-08 Released: 2007-06-26 
• Deposition Author(s): Chopra, R., Bard, J., Svenson, K., Mansour, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.244 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of E. Coli Mur B bound to a napthyl tetronic acid inhibitor

Mansour, T., Caulfield, C.E., Rasmussen, B., Chopra, R., Krishnamurthy, G., Morris, K.M., Svenson, K., Bard, J., Smeltzer, C., Naughton, S., Antane, S., Yang, Y., Severin, A., Quagliato, D., Petersen, P.J., Singh, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.03 kDa 
• Atom Count: 2,956 
• Modeled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylenolpyruvoylglucosamine reductase	A	342	Escherichia coli	Mutation(s): 0  EC: 1.1.1.158 (PDB Primary Data), 1.3.1.98 (UniProt)
UniProt
Find proteins for P08373 (Escherichia coli (strain K12)) Explore P08373  Go to UniProtKB:  P08373

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
973	B [auth A]	(5Z)-3-(4-CHLOROPHENYL)-4-HYDROXY-5-(1-NAPHTHYLMETHYLENE)FURAN-2(5H)-ONE C21 H13 Cl O3 PLGHLEBIWUQEPR-PDGQHHTCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
973	BindingDB:  2Q85	IC50: 2.86e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.244 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.993	α = 90
b = 89.301	β = 111.11
c = 50.943	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Chopra, R., Bard, J., Svenson, K., Mansour, T.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description