Research workbench
Crystal structure of methionyl-tRNA synthetase metrs from brucella melitensis bound to selenomethionine
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
- 4DLP
- Type
- protein
- Length
- 1,425 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoacyl-tRNA synthetase, class I:AMINOACYL-tRNA synthetase, class IA:METHIONYL-tRNA…
- EC
- 6.1.1.10
- UniProt
- Q2YQ76
- Ligands
- MSE
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoacyl-tRNA synthetase, class I:AMINOACYL-tRNA synthetase, class IA:METHIONYL-tRNA synthetase, class ia (EC 6.1.1.10) | protein | 493 | 53% helix, 15% strand | Q2YQ76 |
| B | Aminoacyl-tRNA synthetase, class I:AMINOACYL-tRNA synthetase, class IA:METHIONYL-tRNA synthetase, class ia (EC 6.1.1.10) | protein | 464 | 56% helix, 13% strand | Q2YQ76 |
| C | Aminoacyl-tRNA synthetase, class I:AMINOACYL-tRNA synthetase, class IA:METHIONYL-tRNA synthetase, class ia (EC 6.1.1.10) | protein | 468 | 55% helix, 13% strand | Q2YQ76 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.70 | 0.78 | 74 | MSE |
| 2 | 990 | 0.68 | 0.74 | 69 | empty |
| 3 | 201 | 0.62 | 0.83 | 25 | empty |
| 4 | 207 | 0.62 | 0.82 | 35 | MSE |
| 5 | 210 | 0.62 | 0.82 | 32 | MSE |
Interfaces
2 interfaces between chains.
- A–C · 276 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 156 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4DLP · Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis bound to… · 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 Q2YQ76
- Elsewhere: RCSB PDB 4DLP · PDBe 4DLP · UniProt Q2YQ76
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