4XEM

Crystal Structure of wild type human AlaRS catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb4XEM/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-24 Released: 2016-02-17 
• Deposition Author(s): Zhou, H., He, W., Yang, X.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

Crystal structure of wild type human AlaRS catalytic domain

Zhou, H., Yang, X.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 54.04 kDa 
• Atom Count: 3,595 
• Modelled Residue Count: 377 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine--tRNA ligase, cytoplasmic	A	475	Homo sapiens	Mutation(s): 0  Gene Names: AARS EC: 6.1.1.7 (PDB Primary Data), 6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49588 (Homo sapiens) Explore P49588  Go to UniProtKB:  P49588
PHAROS:  P49588 GTEx:  ENSG00000090861

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A5A	B [auth A]	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S CWWYMWDIYBJVLP-YTMOPEAISA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.121	α = 90
b = 67.131	β = 127.42
c = 75.107	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-17 
Deposition Author(s): Zhou, H., He, W., Yang, X.L.

Revision History  

• Version 1.0: 2016-02-17
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description