5VR8

Human UDP-Glucose Dehydrogenase with UDP-Xylose Bound to the Co-enzyme Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 2.5 of the entry. See complete history

Literature

The entropic force generated by intrinsically disordered segments tunes protein function.

Keul, N.D.Oruganty, K.Schaper Bergman, E.T.Beattie, N.R.McDonald, W.E.Kadirvelraj, R.Gross, M.L.Phillips, R.S.Harvey, S.C.Wood, Z.A.

(2018) Nature 563: 584-588


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-glucose 6-dehydrogenase
A, B, C, D, E, F
495Homo sapiensMutation(s): 0 
Gene Names: UGDH
EC: 1.1.1.22
Find proteins for O60701 (Homo sapiens)
Go to Gene View: UGDH
Go to UniProtKB:  O60701
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
C, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
UDX
Query on UDX

Download SDF File 
Download CCD File 
A, B, C, D, E, F
URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE
UDP-ALPHA-D-XYLOPYRANOSE
C14 H22 N2 O16 P2
DQQDLYVHOTZLOR-OCIMBMBZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.999 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.080α = 90.00
b = 196.490β = 111.91
c = 111.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 2.0: 2018-03-21
    Type: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2018-03-28
    Type: Data collection, Database references
  • Version 2.2: 2018-11-07
    Type: Data collection, Database references
  • Version 2.3: 2018-11-14
    Type: Data collection, Database references
  • Version 2.4: 2018-11-28
    Type: Data collection, Database references
  • Version 2.5: 2018-12-05
    Type: Data collection, Database references