3KFY | pdb_00003kfy

Dynamic switching and partial occupancies of a small molecule inhibitor complex of DHFR

• PDB DOI: https://doi.org/10.2210/pdb3KFY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2009-10-28 Released: 2010-12-08 
• Deposition Author(s): Collins, E.J., Lee, A.L., Carroll, M.J., Gromova, A.V., Miller, K.R., Singleton, S.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Dynamic switching and partial occupancies of a small molecule inhibitor complex of DHFR

Collins, E.J., Lee, A.L., Carroll, M.J., Gromova, A.V., Miller, K.R., Singleton, S.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 19.19 kDa 
• Atom Count: 1,475 
• Modeled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	159	Escherichia coli K-12	Mutation(s): 1  EC: 1.5.1.3
UniProt
Find proteins for P0ABQ4 (Escherichia coli (strain K12)) Explore P0ABQ4  Go to UniProtKB:  P0ABQ4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
JZM	C [auth A]	5-[(4-chlorophenyl)sulfanyl]quinazoline-2,4-diamine C14 H11 Cl N4 S AVRPDIOCAAWICH-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JZM	BindingDB:  3KFY	Ki: 38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.23	α = 90
b = 44.89	β = 90
c = 98.01	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
BUSTER	refinement
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Collins, E.J., Lee, A.L., Carroll, M.J., Gromova, A.V., Miller, K.R., Singleton, S.F.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description