7P7W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 

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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
C [auth AAA],
Z [auth BBB]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
NDG (Subject of Investigation/LOI)
Query on NDG

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

Download Ideal Coordinates CCD File 
W [auth AAA]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth BBB],
D [auth AAA],
G [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
AA [auth BBB],
BA [auth BBB],
E [auth AAA],
F [auth AAA]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN (Subject of Investigation/LOI)
Query on ZN

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

Download Ideal Coordinates CCD File 
GA [auth BBB]
HA [auth BBB]
IA [auth BBB]
JA [auth BBB]
K [auth AAA]
GA [auth BBB],
HA [auth BBB],
IA [auth BBB],
JA [auth BBB],
K [auth AAA],
KA [auth BBB],
L [auth AAA],
M [auth AAA],
N [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA],
R [auth AAA],
S [auth AAA],
T [auth AAA],
U [auth AAA],
V [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
Y [auth BBB]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
LA [auth BBB],
X [auth AAA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.1α = 90
b = 115.1β = 90
c = 120.304γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
xia2data scaling

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: 2022-08-03
    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