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Crystal structure of methionyl-tRNA synthetase metrs from brucella melitensis in complex with inhibitor chem 1312
Analyse Crystal structure of methionyl-tRNA synthetase metrs from brucella melitensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K0S
- Type
- protein
- Length
- 1,478 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
- 0OU
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 496 | 52% helix, 15% strand | P59078 |
| B | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 485 | 53% helix, 15% strand | P59078 |
| C | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 497 | 52% helix, 16% strand | P59078 |
Ligands and binding sites
- 0OU · 2-({3-[(3,5-dichlorobenzyl)amino]propyl}amino)quinolin-4(1H)-one · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.74 | 0.81 | 64 | 0OU |
| 2 | 631 | 0.68 | 0.77 | 57 | empty |
| 3 | 431 | 0.67 | 0.79 | 50 | 0OU |
| 4 | 197 | 0.66 | 0.84 | 34 | 0OU |
| 5 | 250 | 0.64 | 0.81 | 34 | 0OU |
Interfaces
3 interfaces between chains.
- A–B · 352 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 139 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5K0S · 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 0.97
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 5K0S · PDBe 5K0S · UniProt P59078
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