3GG2

Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate

Bonanno, J.B.Freeman, J.Bain, K.T.Chang, S.Sampathkumar, P.Wasserman, S.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sugar dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase familyA, B, C, D450Porphyromonas gingivalisMutation(s): 4 
Gene Names: PGN_1243PG_1143
EC: 1.1.1.22
UniProt
Find proteins for Q7MVC7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MVC7 
Go to UniProtKB:  Q7MVC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MVC7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UGA
Query on UGA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth B],
H [auth C],
I [auth D],
E [auth A],
F [auth A],
G [auth B],
H [auth C],
I [auth D],
J [auth D]
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID
C15 H22 N2 O18 P2
HDYANYHVCAPMJV-LXQIFKJMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.365α = 90
b = 143.489β = 112.46
c = 85.501γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.4: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2021-10-20
    Changes: Database references