5NZG

Crystal structure of UDP-glucose pyrophosphorylase S374W mutant from Leishmania major in complex with UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb5NZG/pdb

Classification: TRANSFERASE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-05-14 Released: 2018-04-18
Deposition Author(s): Cramer, J.T., Fuehring, J.I., Baruch, P., Bruetting, C., Hesse, R., Knoelker, H.-J., Gerardy-Schahn, R., Fedorov, R.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.247
R-Value Work: 0.219
R-Value Observed: 0.221

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies

Cramer, J.T., Fuehring, J.I., Baruch, P., Bruetting, C., Knoelker, H.-J., Gerardy-Schahn, R., Fedorov, R.

(2018) ACS Catal 8

DOI: https://doi.org/10.1021/acscatal.7b03714

Macromolecule Content

Total Structure Weight: 57.53 kDa
Atom Count: 4,234
Modelled Residue Count: 482
Deposited Residue Count: 505
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose pyrophosphorylase	A	505	Leishmania major	Mutation(s): 1 Gene Names: UGP, LMJF_18_0990 EC: 2.7.7.9
UniProt
Find proteins for Q4QDU3 (Leishmania major) Explore Q4QDU3 Go to UniProtKB: Q4QDU3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4QDU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG Query on UPG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.247
R-Value Work: 0.219
R-Value Observed: 0.221
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.5	α = 90
b = 89.8	β = 90
c = 137.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SADABS	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	GZ: FE 1510/2-1

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.2: 2024-10-16
Changes: Structure summary