7P9Y

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG (Subject of Investigation/LOI)
Query on NDG

Download Ideal Coordinates CCD File 
DA [auth BBB],
N [auth AAA]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
PGE
Query on PGE

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

Download Ideal Coordinates CCD File 
C [auth AAA],
M [auth AAA],
W [auth BBB]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
U [auth BBB]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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

Download Ideal Coordinates CCD File 
AA [auth BBB]
BA [auth BBB]
CA [auth BBB]
D [auth AAA]
E [auth AAA]
AA [auth BBB],
BA [auth BBB],
CA [auth BBB],
D [auth AAA],
E [auth AAA],
F [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
R [auth AAA],
V [auth BBB],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
GA [auth BBB],
Q [auth AAA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.476α = 90
b = 115.476β = 90
c = 119.657γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-02-07
    Changes: Refinement description