MolNFT v1 · #110974 · protein
Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase
4YCU · Lysine--tRNA ligase: “Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase”. X-ray diffraction, 2 ligands (KRS, LYS), 15 pockets (best druggability 0.84). MolNFT v1 #110974 on GenesisL1: 3D structure, binding…
- PDB
- 4YCU
- Type
- protein
- Length
- 1,035 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase; Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
- EC
- 6.1.1.6
- UniProt
- Q15046, Q13155
- Ligands
- KRS, LYS
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 505 | 35% helix, 25% strand | Q15046 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 499 | 36% helix, 26% strand | Q15046 |
| C | Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | protein | 31 | 0% helix, 0% strand | Q13155 |
Ligands and binding sites
- KRS · cladosporin · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.84 | 0.97 | 55 | empty |
| 2 | 779 | 0.79 | 0.83 | 74 | KRS, LYS, GOL |
| 3 | 793 | 0.77 | 0.81 | 73 | KRS, LYS, GOL |
| 4 | 277 | 0.74 | 0.87 | 36 | empty |
| 5 | 230 | 0.72 | 0.87 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4438 Ų buried · 77 hydrogen bonds · protein-protein
- A–C · 741 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 409 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YCU · Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase · the same entry in another collection · chain B against B, TM-score 1.00
- Q15046 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q15046) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q13155 · AlphaFold monomer V2.0 prediction for aminoacyl tRNA synthase complex-interacting… · a predicted model of the same protein · chain C against A, TM-score 0.25
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15046
- Every structure of UniProt Q13155
- Elsewhere: RCSB PDB 4YCU · PDBe 4YCU · UniProt Q15046 · UniProt Q13155
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