MolNFT v1 · #190257 · protein
Methionyl-tRNA synthetase from staphylococcus aureus complexed with a phenylbenzimidazole inhibitor and ATP
7WPN · Methionine--tRNA ligase: “Methionyl-tRNA synthetase from staphylococcus aureus complexed with a phenylbenzimidazole inhibitor and ATP”. X-ray diffraction, 2 ligands (ATP, 29I), 4 pockets (best druggability 0.65). MolNFT v1 #190257…
- PDB
- 7WPN
- Type
- protein
- Length
- 478 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
- ATP, 29I
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 478 | 53% helix, 13% strand | Q5HII6 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 29I · (phenylmethyl) N-[(2R)-2-[2-(4-bromanyl-3-oxidanyl-phenyl)-5-(methylcarbamoyl)benzimidazol-1-yl]-2-(3,4-dimethoxyphenyl)ethyl]carbamate · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.65 | 0.80 | 41 | ATP, 29I |
| 2 | 75 | 0.43 | 0.80 | 17 | empty |
| 3 | 66 | 0.38 | 0.78 | 13 | empty |
| 4 | 55 | 0.30 | 0.75 | 12 | empty |
Compared structures
- 7WPN · 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 7WPN · PDBe 7WPN · UniProt Q5HII6
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