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

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56192
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MET Query on MET Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.