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 1.1 of the entry. See complete history.

Literature

Co-Translational Deposition of N6-Acetyl-L-Lysine in Nascent Proteins Contributes to the Acetylome in Mammalian Cells

Guo, D., Li, N., Zhang, X., Zhou, R., He, J., Ding, X.P., Yu, W., Tong, F., Yin, S., Wang, Y., Xu, X., Wang, L., Fan, M., Feng, S., Liu, K., Tang, K., Ouyang, Z., Guo, Y.R., Wang, Y.

(2025) Adv Sci (Weinh) 12: 2403309

DOI: https://doi.org/10.1002/advs.202403309

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
Version 1.1: 2026-02-04
Changes: Database references

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.