6C5Z

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


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
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The A225L Substitution of hUGDH alters structure and function

Gross, P.G.Wood, Z.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glucose 6-dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
494Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60701
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
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
Query on UPG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
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 = 93.77α = 90
b = 199.8β = 90
c = 200.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM114298

Revision History  (Full details and data files)

  • 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