6KD9 | pdb_00006kd9

Binding pose 1 of 2-CF3 bound AsqJ complex

• PDB DOI: https://doi.org/10.2210/pdb6KD9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-01 Released: 2020-03-18 
• Deposition Author(s): Liao, H.J., Chan, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.285 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Binding pose 1 of 2-CF3 bound AsqJ complex

Liao, H.J., Chan, N.L.

(2020) J Am Chem Soc 

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: 73.25 kDa 
• Atom Count: 4,545 
• Modeled Residue Count: 574 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron/alpha-ketoglutarate-dependent dioxygenase asqJ	A [auth B], B [auth F]	327	Aspergillus nidulans FGSC A4	Mutation(s): 0  Gene Names: asqJ, AN9227 EC: 1.14 (PDB Primary Data), 1.14.11.81 (UniProt)
UniProt
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q5AR53  Go to UniProtKB:  Q5AR53

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CV3 (Subject of Investigation/LOI)	D [auth B], G [auth F]	(3~{Z})-4-methyl-3-[[4-(trifluoromethyl)phenyl]methylidene]-1~{H}-1,4-benzodiazepine-2,5-dione C18 H13 F3 N2 O2 NVEJUUHKRHQWHW-GDNBJRDFSA-N
SIN	E [auth B], H [auth F]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
FE	C [auth B], F	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.285 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.755	α = 90
b = 73.352	β = 90
c = 121.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Liao, H.J., Chan, N.L.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-03-20
  Changes: Source and taxonomy