7PA1

Structure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate

PDB DOI: https://doi.org/10.2210/pdb7PA1/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: 2.20 Å
R-Value Free: 0.252
R-Value Work: 0.208

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

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

Macromolecule Content

Total Structure Weight: 94.44 kDa
Atom Count: 4,972
Modelled Residue Count: 608
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	R8APY9Q12306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain L [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain L [auth BBB]	D [auth AAA], L [auth BBB]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth AAA] Focus chain L [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain L [auth BBB]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain N [auth BBB] SDF format, chain O [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain O [auth BBB]	F [auth AAA], G [auth AAA], N [auth BBB], O [auth BBB]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain N [auth BBB] Focus chain O [auth BBB]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain K [auth BBB]	C [auth AAA], K [auth BBB]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain K [auth BBB]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain M [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain M [auth BBB]	E [auth AAA], M [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain M [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain M [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] SDF format, chain U [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain U [auth BBB]	H [auth AAA] I [auth AAA] J [auth AAA] P [auth BBB] Q [auth BBB] H [auth AAA], I [auth AAA], J [auth AAA], P [auth BBB], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB], U [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain U [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252
R-Value Work: 0.208
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.265	α = 90
b = 121.265	β = 90
c = 91.684	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

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