MolNFT v1 · #123961 · protein
Crystal structure of methionyl-tRNA synthetase metrs from brucella melitensis in complex with inhibitor chem 1415
5K0T · Methionine--tRNA ligase: “Crystal structure of methionyl-tRNA synthetase metrs from brucella melitensis in complex with inhibitor chem…”. X-ray diffraction, 1 ligand (415), 9 pockets (best druggability 0.68). MolNFT v1 #123961 on…
- PDB
- 5K0T
- Type
- protein
- Length
- 1,445 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine--tRNA ligase
- EC
- 6.1.1.10
- UniProt
- P59078
- Ligands
- 415
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 496 | 53% helix, 15% strand | P59078 |
| B | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 468 | 56% helix, 14% strand | P59078 |
| C | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 481 | 54% helix, 14% strand | P59078 |
Ligands and binding sites
- 415 · 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.68 | 0.75 | 72 | empty |
| 2 | 594 | 0.68 | 0.77 | 53 | empty |
| 3 | 556 | 0.67 | 0.77 | 58 | 415 |
| 4 | 306 | 0.66 | 0.81 | 49 | 415 |
| 5 | 328 | 0.65 | 0.80 | 49 | 415 |
Interfaces
3 interfaces between chains.
- A–B · 391 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 173 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5K0T · Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P59078 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (P59078) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P59078
- Elsewhere: RCSB PDB 5K0T · PDBe 5K0T · UniProt P59078
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