7P7I

Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases

Cross, A.R.Roy, S.Vivoli Vega, M.Rejzek, M.Nepogodiev, S.A.Cliff, M.Salmon, D.Isupov, M.N.Field, R.A.Prior, J.L.Harmer, N.J.

(2022) J Biol Chem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinaseA [auth AAA],
B [auth BBB]
417Saccharomyces cerevisiae S288CPlesiomonas shigelloides 302-73
This entity is chimeric
Mutation(s): 0 
Gene Names: SMT3YDR510WD9719.15nagKPLESHI_11010
EC: 2.7.1.59
UniProt
Find proteins for R8APY9 (Plesiomonas shigelloides 302-73)
Explore R8APY9 
Go to UniProtKB:  R8APY9
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsR8APY9Q12306
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth AAA],
O [auth BBB]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth AAA]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA],
M [auth BBB]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth AAA],
N [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
P [auth BBB]
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
P [auth BBB],
Q [auth BBB],
R [auth BBB],
S [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.23α = 90
b = 95.23β = 90
c = 180.55γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMmodel building
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N001591/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-02-15
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Refinement description