1VM8 | pdb_00001vm8

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine pyrophosphorylase	A, B	534	Mus musculus	Mutation(s): 13  EC: 2.7.7.23 (PDB Primary Data), 2.7.7.83 (UniProt), 2.7.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YN5 (Mus musculus) Explore Q91YN5  Go to UniProtKB:  Q91YN5
IMPC:  MGI:1334459

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VM8

Space Group: P 1 2₁ 1

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary