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Crystal structure of methionyl-tRNA synthetase (metrs) from acinetobacter baumannii with bound L-methionine
Analyse Crystal structure of methionyl-tRNA synthetase (metrs) from acinetobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5URB
- Type
- protein
- Length
- 1,092 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine--tRNA ligase
- EC
- 6.1.1.10
- UniProt
- A0A0D5YKJ7
- Ligands
- MET, NA, ZN, NO3
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 546 | 49% helix, 16% strand | A0A0D5YKJ7 |
Ligands and binding sites
- MET · Methionine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.72 | 0.78 | 75 | MET, NO3 |
| 2 | 490 | 0.63 | 0.76 | 43 | NO3 |
| 3 | 332 | 0.63 | 0.79 | 34 | MET |
| 4 | 187 | 0.62 | 0.83 | 38 | EDO |
| 5 | 145 | 0.42 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5URB · Crystal Structure of Methionyl-tRNA synthetase (MetRS) from Acinetobacter baumannii with… · 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 A0A0D5YKJ7
- Elsewhere: RCSB PDB 5URB · PDBe 5URB · UniProt A0A0D5YKJ7
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