Download MendeleyCrystal Structure of human lysyl-tRNA synthetase with acetyllysine
Zhang, X., Li, N., Guo, Y.R., Ouyang, Z.To be published.
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
- 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
View more details
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lysine--tRNA ligase | 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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ALY (Subject of Investigation/LOI) Query on ALY | C [auth A], D [auth B] | N(6)-ACETYLLYSINE C8 H16 N2 O3 DTERQYGMUDWYAZ-ZETCQYMHSA-N |  | ||
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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-01-22 Deposition Author(s): Zhang, X., Li, N., Guo, Y.R., Ouyang, Z.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-01-22
Type: Initial release
