5NZM | pdb_00005nzm

Crystal structure of UDP-glucose pyrophosphorylase from Leishmania major in complex with murrayamine-I

PDB DOI: https://doi.org/10.2210/pdb5NZM/pdb

Classification: TRANSFERASE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

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: 2.35 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 56.39 kDa
Atom Count: 3,769
Modeled Residue Count: 483
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): 0 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9ET Query on 9ET 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]	Murrayamine-I C₂₀ H₁₉ N O₄ HGIQTDGMLIBTAD-HXUWFJFHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.224 (Depositor), 0.220 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.11	α = 90
b = 95.11	β = 90
c = 72.67	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):

Knoelker, H.-J.

Gerardy-Schahn, R.

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, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.