Macromolecule Content

Total Structure Weight: 122.06 kDa
Atom Count: 7,644
Modelled Residue Count: 981
Deposited Residue Count: 1,068
Unique protein chains: 1

1VM8

Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VM8/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-09-10 Released: 2004-10-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine pyrophosphorylase	A, B	534	Mus musculus	Mutation(s): 13 Gene Names: Uap1 EC: 2.7.7.23 (PDB Primary Data), 2.7.7.83 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YN5 (Mus musculus) Explore Q91YN5 Go to UniProtKB: Q91YN5
IMPC: MGI:1334459
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q91YN5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B]	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.266
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M31VM8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.094	α = 90
b = 73.402	β = 99.83
c = 107.132	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-10-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-10-05
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.