Research workbench
Methionyl-tRNA synthetase from staphylococcus aureus complexed with a phenylbenzimidazole inhibitor
Analyse Methionyl-tRNA synthetase from staphylococcus aureus complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPI
- Type
- protein
- Length
- 520 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methionine--tRNA ligase
- EC
- 6.1.1.10
- UniProt
- Q5HII6
- Ligands
- 1V7
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 520 | 50% helix, 17% strand | Q5HII6 |
Ligands and binding sites
- 1V7 · 2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl) ethyl]-N-methyl-benzimidazole-5-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.73 | 0.77 | 73 | 1V7, EDO |
| 2 | 55 | 0.42 | 0.82 | 13 | empty |
| 3 | 53 | 0.27 | 0.74 | 13 | empty |
Compared structures
- 7WPI · Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HII6 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (Q5HII6) · a predicted model of the same protein · chain A 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 Q5HII6
- Elsewhere: RCSB PDB 7WPI · PDBe 7WPI · UniProt Q5HII6
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