8XP4 | pdb_00008xp4

Crystal Structure of human lysyl-tRNA synthetase with acetyllysine

PDB DOI: https://doi.org/10.2210/pdb8XP4/pdb

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

Deposited: 2024-01-03 Released: 2025-01-22
Deposition Author(s): Zhang, X., Li, N., Guo, Y.R., Ouyang, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.239 (Depositor), 0.239 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of human lysyl-tRNA synthetase with acetyllysine

Zhang, X., Li, N., Guo, Y.R., Ouyang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 120.77 kDa
Atom Count: 8,173
Modeled Residue Count: 979
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B	520	Homo sapiens	Mutation(s): 0 Gene Names: KARS1, KARS, KIAA0070 EC: 2.7.7 (PDB Primary Data), 6.1.1.6 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15046 (Homo sapiens) Explore Q15046 Go to UniProtKB: Q15046
PHAROS: Q15046 GTEx: ENSG00000065427
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15046
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ALY (Subject of Investigation/LOI) Query on ALY Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N(6)-ACETYLLYSINE C₈ H₁₆ N₂ O₃ DTERQYGMUDWYAZ-ZETCQYMHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.239 (Depositor), 0.239 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.337	α = 90
b = 90.469	β = 90
c = 107.201	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.