4H7U

Crystal structure of pyranose dehydrogenase from Agaricus meleagris, wildtype


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 4H7U

Classification: OXIDOREDUCTASE

Total Structure Weight: 66310.74

Macromolecule Entities
Molecule Chains Length Organism Details
Pyranose dehydrogenase A 602 Leucoagaricus meleagris EC#: 1.1.99.29 IUBMB
Gene Name(s): pdh1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FED
Query on FED

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
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.171
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 51.94 α = 90.00
b = 74.64 β = 90.00
c = 139.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-20
  • 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

    Type: Data collection, Refinement description