4H7U

Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype

• PDB DOI: https://doi.org/10.2210/pdb4H7U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leucoagaricus meleagris
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2012-09-20 Released: 2013-08-07 
• Deposition Author(s): Tan, T.C., Spadiut, O., Divne, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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: 66.29 kDa 
• Atom Count: 5,014 
• Modelled Residue Count: 577 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyranose dehydrogenase	A	602	Leucoagaricus meleagris	Mutation(s): 0  Gene Names: pdh1 EC: 1.1.99.29
UniProt
Find proteins for Q3L245 (Leucoagaricus meleagris) Explore Q3L245  Go to UniProtKB:  Q3L245

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FED	C [auth A]	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aR)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate (non-preferred name) C27 H35 N9 O16 P2 WTOYVZYXGAOYIM-QUWWARRSSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.938	α = 90
b = 74.64	β = 90
c = 139.286	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Tan, T.C., Spadiut, O., Divne, C.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Data collection, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary