4M2B | pdb_00004m2b

Crystal structure of L281D mutant of udp-glucose pyrophosphorylase from leishmania major in complex with udp-glc

PDB DOI: https://doi.org/10.2210/pdb4M2B/pdb

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

Deposited: 2013-08-05 Released: 2014-01-29
Deposition Author(s): Fuehring, J., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.242 (Depositor), 0.198 (DCC)
R-Value Work:
0.175 (Depositor)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Catalytic Mechanism and Allosteric Regulation of Udp-Glucose Pyrophosphorylase from Leishmania Major

Fuehring, J., Routier, F.H., Lamerz, A.-C., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

(2013) ACS Catal 36329: 2976-2985

DOI: https://doi.org/10.1021/cs4007777

Macromolecule Content

Total Structure Weight: 56.62 kDa
Atom Count: 4,159
Modeled Residue Count: 483
Deposited Residue Count: 505
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose pyrophosphorylase	A	505	Leishmania major	Mutation(s): 1 Gene Names: LMJF_18_0990, UGP EC: 2.7.7.9
UniProt
Find proteins for Q4QDU3 (Leishmania major) Explore Q4QDU3 Go to UniProtKB: Q4QDU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QDU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242 (Depositor), 0.198 (DCC)
R-Value Work: 0.175 (Depositor)
R-Value Observed: 0.178 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.79	α = 90
b = 86.9	β = 90
c = 138.23	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
CCP4	model building
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Gerardy-Schahn, R.

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2014-02-19
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.