1GQH

Quercetin 2,3-dioxygenase in complex with the inhibitor kojic acid

• PDB DOI: https://doi.org/10.2210/pdb1GQH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus japonicus
• Expression System: Aspergillus awamori
• Mutation(s): No 


• Deposited: 2001-11-23 Released: 2002-06-21 
• Deposition Author(s): Steiner, R.A., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 157.82 kDa 
• Atom Count: 11,746 
• Modelled Residue Count: 1,339 
• Deposited Residue Count: 1,400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
QUERCETIN 2,3-DIOXYGENASE	A, B, C, D	350	Aspergillus japonicus	Mutation(s): 0  EC: 1.13.11.24
UniProt
Find proteins for Q7SIC2 (Aspergillus japonicus) Explore Q7SIC2  Go to UniProtKB:  Q7SIC2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth D], BA [auth D], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
KOJ	I [auth A], O [auth B], T [auth C], Y [auth D]	5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE C6 H6 O4 BEJNERDRQOWKJM-UHFFFAOYSA-N
CU	J [auth A], P [auth B], U [auth C], Z [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.64	α = 90
b = 55.396	β = 98.26
c = 124.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-21 
Deposition Author(s): Steiner, R.A., Dijkstra, B.W.

Revision History  

• Version 1.0: 2002-06-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary