7P9L | pdb_00007p9l

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

PDB DOI: https://doi.org/10.2210/pdb7P9L/pdb

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

Deposited: 2021-07-27 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: 1.75 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (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: 95.32 kDa
Atom Count: 5,453
Modeled Residue Count: 609
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
4QY (Subject of Investigation/LOI) Query on 4QY Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain CA [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain CA [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain CA [auth BBB]	CA [auth BBB], F [auth AAA]	2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose C₈ H₁₆ N O₉ P BRGMHAYQAZFZDJ-FMDGEEDCSA-N		Interactions Focus chain CA [auth BBB] Focus chain F [auth AAA] Interactions & Density Focus chain CA [auth BBB] Focus chain F [auth AAA]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain DA [auth BBB] MOL2 format, chain DA [auth BBB] mmCIF format, chain DA [auth BBB]	DA [auth BBB]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain DA [auth BBB] Interactions & Density Focus chain DA [auth BBB]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth BBB] SDF format, chain X [auth BBB] SDF format, chain LA [auth BBB] SDF format, chain KA [auth BBB] SDF format, chain FA [auth BBB] SDF format, chain E [auth AAA] SDF format, chain BA [auth BBB] MOL2 format, chain Y [auth BBB] MOL2 format, chain X [auth BBB] MOL2 format, chain LA [auth BBB] MOL2 format, chain KA [auth BBB] MOL2 format, chain FA [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain BA [auth BBB] mmCIF format, chain Y [auth BBB] mmCIF format, chain X [auth BBB] mmCIF format, chain LA [auth BBB] mmCIF format, chain KA [auth BBB] mmCIF format, chain FA [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain BA [auth BBB]	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		Interactions Focus chain BA [auth BBB] Focus chain E [auth AAA] Focus chain FA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain X [auth BBB] Focus chain Y [auth BBB] Interactions & Density Focus chain BA [auth BBB] Focus chain E [auth AAA] Focus chain FA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain X [auth BBB] Focus chain Y [auth BBB]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth AAA] SDF format, chain QA [auth BBB] MOL2 format, chain V [auth AAA] MOL2 format, chain QA [auth BBB] mmCIF format, chain V [auth AAA] mmCIF format, chain QA [auth BBB]	QA [auth BBB], V [auth AAA]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain QA [auth BBB] Focus chain V [auth AAA] Interactions & Density Focus chain QA [auth BBB] Focus chain V [auth AAA]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth AAA] SDF format, chain Q [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain NA [auth BBB] MOL2 format, chain R [auth AAA] MOL2 format, chain Q [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain NA [auth BBB] mmCIF format, chain R [auth AAA] mmCIF format, chain Q [auth AAA] mmCIF format, chain OA [auth BBB] mmCIF format, chain NA [auth BBB]	NA [auth BBB], OA [auth BBB], Q [auth AAA], R [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain NA [auth BBB] Focus chain OA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA] Interactions & Density Focus chain NA [auth BBB] Focus chain OA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth BBB] SDF format, chain U [auth AAA] SDF format, chain S [auth AAA] SDF format, chain P [auth AAA] SDF format, chain O [auth AAA] SDF format, chain N [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain M [auth AAA] SDF format, chain L [auth AAA] SDF format, chain K [auth AAA] SDF format, chain JA [auth BBB] SDF format, chain J [auth AAA] SDF format, chain IA [auth BBB] SDF format, chain I [auth AAA] SDF format, chain HA [auth BBB] SDF format, chain H [auth AAA] SDF format, chain GA [auth BBB] SDF format, chain G [auth AAA] SDF format, chain EA [auth BBB] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] SDF format, chain AA [auth BBB] MOL2 format, chain Z [auth BBB] MOL2 format, chain U [auth AAA] MOL2 format, chain S [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain JA [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain IA [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain HA [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain GA [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain EA [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain AA [auth BBB] mmCIF format, chain Z [auth BBB] mmCIF format, chain U [auth AAA] mmCIF format, chain S [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain MA [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain JA [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain IA [auth BBB] mmCIF format, chain I [auth AAA] mmCIF format, chain HA [auth BBB] mmCIF format, chain H [auth AAA] mmCIF format, chain GA [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain EA [auth BBB] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain AA [auth BBB]	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		Interactions Focus chain AA [auth BBB] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain EA [auth BBB] Focus chain G [auth AAA] Focus chain GA [auth BBB] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain S [auth AAA] Focus chain U [auth AAA] Focus chain Z [auth BBB] Interactions & Density Focus chain AA [auth BBB] Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain EA [auth BBB] Focus chain G [auth AAA] Focus chain GA [auth BBB] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain S [auth AAA] Focus chain U [auth AAA] Focus chain Z [auth BBB]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain T [auth AAA] SDF format, chain PA [auth BBB] MOL2 format, chain T [auth AAA] MOL2 format, chain PA [auth BBB] mmCIF format, chain T [auth AAA] mmCIF format, chain PA [auth BBB]	PA [auth BBB], T [auth AAA]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain PA [auth BBB] Focus chain T [auth AAA] Interactions & Density Focus chain PA [auth BBB] Focus chain T [auth AAA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth AAA] MOL2 format, chain W [auth AAA] mmCIF format, chain W [auth AAA]	W [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth AAA] Interactions & Density Focus chain W [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.508	α = 90
b = 114.508	β = 90
c = 119.266	γ = 120

Software Package:

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

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