7P9L

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 

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
4QY (Subject of Investigation/LOI)
Query on 4QY

Download Ideal Coordinates CCD File 
CA [auth BBB],
F [auth AAA]
2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose
C8 H16 N O9 P
BRGMHAYQAZFZDJ-FMDGEEDCSA-N
TRS
Query on TRS

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

Download Ideal Coordinates CCD File 
BA [auth BBB]
E [auth AAA]
FA [auth BBB]
KA [auth BBB]
LA [auth BBB]
BA [auth BBB],
E [auth AAA],
FA [auth BBB],
KA [auth BBB],
LA [auth BBB],
X [auth BBB],
Y [auth BBB]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
QA [auth BBB],
V [auth AAA]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

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

Download Ideal Coordinates CCD File 
AA [auth BBB]
C [auth AAA]
D [auth AAA]
EA [auth BBB]
G [auth AAA]
AA [auth BBB],
C [auth AAA],
D [auth AAA],
EA [auth BBB],
G [auth AAA],
GA [auth BBB],
H [auth AAA],
HA [auth BBB],
I [auth AAA],
IA [auth BBB],
J [auth AAA],
JA [auth BBB],
K [auth AAA],
L [auth AAA],
M [auth AAA],
MA [auth BBB],
N [auth AAA],
O [auth AAA],
P [auth AAA],
S [auth AAA],
U [auth AAA],
Z [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.508α = 90
b = 114.508β = 90
c = 119.266γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing

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