6C5Z

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound

• PDB DOI: https://doi.org/10.2210/pdb6C5Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-01-17 Released: 2019-01-23 
• Deposition Author(s): Gross, P.G., Sidlo, A.M., Walsh, R.M., Peeples, W.B., Wood, Z.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

The A225L Substitution of hUGDH alters structure and function

Gross, P.G., Wood, Z.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 337.54 kDa 
• Atom Count: 21,261 
• Modelled Residue Count: 2,612 
• Deposited Residue Count: 2,964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 6-dehydrogenase	A, B, C, D, E, F	494	Homo sapiens	Mutation(s): 1  Gene Names: UGDH EC: 1.1.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for O60701 (Homo sapiens) Explore O60701  Go to UniProtKB:  O60701
PHAROS:  O60701 GTEx:  ENSG00000109814

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	G [auth A], J [auth C], L [auth D], N [auth E], P [auth F]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
UPG	H [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.77	α = 90
b = 199.8	β = 90
c = 200.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Gross, P.G., Sidlo, A.M., Walsh, R.M., Peeples, W.B., Wood, Z.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM114298

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description