6Z2F | pdb_00006z2f

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC

• PDB DOI: https://doi.org/10.2210/pdb6Z2F/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-15 Released: 2021-05-26 
• Deposition Author(s): Chen, X., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human AGX1 mutant complexed with UDPGLCNAC

Chen, X., van Aalten, D.M.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 116.37 kDa 
• Atom Count: 8,314 
• Modeled Residue Count: 944 
• Deposited Residue Count: 1,018 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylhexosamine pyrophosphorylase	A	509	Homo sapiens	Mutation(s): 1  Gene Names: UAP1, SPAG2 EC: 2.7.7.83 (PDB Primary Data), 2.7.7.23 (PDB Primary Data), 2.7.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16222 (Homo sapiens) Explore Q16222  Go to UniProtKB:  Q16222
PHAROS:  Q16222 GTEx:  ENSG00000117143

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylhexosamine pyrophosphorylase	B	509	Homo sapiens	Mutation(s): 1  Gene Names: UAP1, SPAG2 EC: 2.7.7.83 (PDB Primary Data), 2.7.7.23 (PDB Primary Data), 2.7.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16222 (Homo sapiens) Explore Q16222  Go to UniProtKB:  Q16222
PHAROS:  Q16222 GTEx:  ENSG00000117143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1	C [auth A], D [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	B	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.614	α = 95.63
b = 64.569	β = 101.09
c = 82.07	γ = 104.93

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Chen, X., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description