7P9Y | pdb_00007p9y

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

PDB DOI: https://doi.org/10.2210/pdb7P9Y/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, Plesiomonas shigelloides 302-73
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-28 Released: 2022-08-10
Deposition Author(s): Roy, S., Isupov, M.N., Harmer, N.J., Ames, J.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)

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 Biological Chem

DOI: https://doi.org/10.1016/j.jbc.2022.101903

Macromolecule Content

Total Structure Weight: 94.38 kDa
Atom Count: 5,095
Modeled Residue Count: 608
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase	A [auth AAA], B [auth BBB]	417	Saccharomyces cerevisiae S288C, Plesiomonas shigelloides 302-73 This entity is chimeric	Mutation(s): 0 Gene Names: SMT3, YDR510W, D9719.15, nagK, PLESHI_11010 EC: 2.7.1.59
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12306 Go to UniProtKB: Q12306
Find proteins for R8APY9 (Plesiomonas shigelloides 302-73) Explore R8APY9 Go to UniProtKB: R8APY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	R8APY9 Q12306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG (Subject of Investigation/LOI) Query on NDG Download:Ideal Coordinates CCD File SDF format, chain DA [auth BBB] SDF format, chain N [auth AAA] MOL2 format, chain DA [auth BBB] MOL2 format, chain N [auth AAA] mmCIF format, chain DA [auth BBB] mmCIF format, chain N [auth AAA]	DA [auth BBB], N [auth AAA]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain DA [auth BBB] Focus chain N [auth AAA] Interactions & Density Focus chain DA [auth BBB] Focus chain N [auth AAA]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain M [auth AAA] SDF format, chain W [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain W [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain W [auth BBB]	C [auth AAA], M [auth AAA], W [auth BBB]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth AAA] Focus chain M [auth AAA] Focus chain W [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain M [auth AAA] Focus chain W [auth BBB]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain U [auth BBB] MOL2 format, chain U [auth BBB] mmCIF format, chain U [auth BBB]	U [auth BBB]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain U [auth BBB] Interactions & Density Focus chain U [auth BBB]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain EA [auth BBB] SDF format, chain FA [auth BBB] SDF format, chain O [auth AAA] SDF format, chain P [auth AAA] MOL2 format, chain EA [auth BBB] MOL2 format, chain FA [auth BBB] MOL2 format, chain O [auth AAA] MOL2 format, chain P [auth AAA] mmCIF format, chain EA [auth BBB] mmCIF format, chain FA [auth BBB] mmCIF format, chain O [auth AAA] mmCIF format, chain P [auth AAA]	EA [auth BBB], FA [auth BBB], O [auth AAA], P [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth BBB] Focus chain FA [auth BBB] Focus chain O [auth AAA] Focus chain P [auth AAA] Interactions & Density Focus chain EA [auth BBB] Focus chain FA [auth BBB] Focus chain O [auth AAA] Focus chain P [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain BA [auth BBB] SDF format, chain CA [auth BBB] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain R [auth AAA] SDF format, chain V [auth BBB] SDF format, chain X [auth BBB] SDF format, chain Y [auth BBB] SDF format, chain Z [auth BBB] MOL2 format, chain AA [auth BBB] MOL2 format, chain BA [auth BBB] MOL2 format, chain CA [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain V [auth BBB] MOL2 format, chain X [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain Z [auth BBB] mmCIF format, chain AA [auth BBB] mmCIF format, chain BA [auth BBB] mmCIF format, chain CA [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain V [auth BBB] mmCIF format, chain X [auth BBB] mmCIF format, chain Y [auth BBB] mmCIF format, chain Z [auth BBB]	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		Interactions Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain R [auth AAA] Focus chain V [auth BBB] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain R [auth AAA] Focus chain V [auth BBB] Focus chain X [auth BBB] Focus chain Y [auth BBB] Focus chain Z [auth BBB]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain GA [auth BBB] SDF format, chain Q [auth AAA] MOL2 format, chain GA [auth BBB] MOL2 format, chain Q [auth AAA] mmCIF format, chain GA [auth BBB] mmCIF format, chain Q [auth AAA]	GA [auth BBB], Q [auth AAA]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth BBB] Focus chain Q [auth AAA] Interactions & Density Focus chain GA [auth BBB] Focus chain Q [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth AAA] SDF format, chain T [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain T [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain T [auth AAA]	S [auth AAA], T [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth AAA] Focus chain T [auth AAA] Interactions & Density Focus chain S [auth AAA] Focus chain T [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.476	α = 90
b = 115.476	β = 90
c = 119.657	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
DM	phasing
MOLREP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/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