2ZXF

Crystal structure of human glycyl-trna synthetase (GLYRS) in complex with AP4A (cocrystallized with AP4A)

• PDB DOI: https://doi.org/10.2210/pdb2ZXF/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-23 Released: 2009-08-25 
• Deposition Author(s): Guo, R.T., Yang, X.L., Schimmel, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.288 
• R-Value Work: 0.244 

Starting Model: experimental

Literature

Crystal structures and biochemical analyses suggest unique mechanism and role for human GlyRS in Ap4A homeostasis

Guo, R.T., Chong, Y.E., Guo, M., Yang, X.L.

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: 79.54 kDa 
• Atom Count: 4,352 
• Modelled Residue Count: 530 
• Deposited Residue Count: 693 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycyl-tRNA synthetase	A	693	Homo sapiens	Mutation(s): 0  Gene Names: GARS EC: 6.1.1.14 (PDB Primary Data), 2.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P41250 (Homo sapiens) Explore P41250  Go to UniProtKB:  P41250
PHAROS:  P41250 GTEx:  ENSG00000106105

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4P	B [auth A]	BIS(ADENOSINE)-5'-TETRAPHOSPHATE C20 H28 N10 O19 P4 YOAHKNVSNCMZGQ-XPWFQUROSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.288 
• R-Value Work: 0.244 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.299	α = 90
b = 137.03	β = 90
c = 132.751	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
XTALVIEW	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Guo, R.T., Yang, X.L., Schimmel, P.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description