MolNFT v1 · #110975 · protein
Crystal structure of cladosporin in complex with plasmodium lysyl-tRNA synthetase
4YCV · Lysine--tRNA ligase: “Crystal structure of cladosporin in complex with plasmodium lysyl-tRNA synthetase”. X-ray diffraction, 1 ligand (KRS), 20 pockets (best druggability 0.82). MolNFT v1 #110975 on GenesisL1: 3D structure, binding…
- PDB
- 4YCV
- Type
- protein
- Length
- 1,935 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- W7JP72
- Ligands
- KRS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 31% helix, 25% strand | W7JP72 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 486 | 31% helix, 26% strand | W7JP72 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 485 | 30% helix, 25% strand | W7JP72 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 479 | 32% helix, 26% strand | W7JP72 |
Ligands and binding sites
- KRS · cladosporin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.82 | 0.97 | 51 | empty |
| 2 | 182 | 0.81 | 0.96 | 41 | empty |
| 3 | 960 | 0.79 | 0.81 | 94 | KRS |
| 4 | 837 | 0.78 | 0.81 | 95 | KRS |
| 5 | 806 | 0.75 | 0.79 | 80 | KRS |
Interfaces
3 interfaces between chains.
- C–D · 4605 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4566 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 152 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4YCV · Crystal structure of cladosporin in complex with plasmodium lysyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
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 W7JP72
- Elsewhere: RCSB PDB 4YCV · PDBe 4YCV · UniProt W7JP72
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