5GL7

Crystal structure of a truncated human cytosolic methionyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb5GL7/pdb

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


• Deposited: 2016-07-08 Released: 2017-07-12 
• Deposition Author(s): Cho, H.Y., Lee, H.J., Kang, B.S.
• Funding Organization(s): National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Crystal structure of a truncated human cytosolic methionyl-tRNA synthetase

Cho, H.Y., Lee, H.J., Kang, B.S.

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: 71.36 kDa 
• Atom Count: 5,138 
• Modelled Residue Count: 597 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase, cytoplasmic	A	624	Homo sapiens	Mutation(s): 0  Gene Names: MARS EC: 6.1.1.10
UniProt & NIH Common Fund Data Resources
Find proteins for P56192 (Homo sapiens) Explore P56192  Go to UniProtKB:  P56192
PHAROS:  P56192 GTEx:  ENSG00000166986

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.035	α = 90
b = 93.03	β = 90
c = 122.084	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Cho, H.Y., Lee, H.J., Kang, B.S.

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Funding Organization	Location	Grant Number
National Research Foundation	Korea, Republic Of	NRF-2014M3A6A4062857

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description