5GOY

The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine

• PDB DOI: https://doi.org/10.2210/pdb5GOY/pdb

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


• Deposited: 2016-07-30 Released: 2017-08-02 
• Deposition Author(s): Lee, H.J., Cho, H.Y., Kang, B.S.
• Funding Organization(s): National Research Foundation of Korea

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.242 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine

Lee, H.J., Cho, H.Y., 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: 71.32 kDa 
• Atom Count: 5,022 
• Modelled Residue Count: 598 
• 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
MET	D [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.242 
• R-Value Work: 0.196 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.539	α = 90
b = 93.133	β = 90
c = 122.482	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: 2017-08-02 
Deposition Author(s): Lee, H.J., Cho, H.Y., Kang, B.S.

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Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	NRF-2015R1A4A1042271

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description