MolNFT v1 · #168776 · protein
Xanthomonas citri methionyl-tRNA synthetase in complex with REP8839
6WQS · Methionine--tRNA ligase: “Xanthomonas citri methionyl-tRNA synthetase in complex with REP8839”. X-ray diffraction, 2 ligands (U7S, ZN), 2 pockets (best druggability 0.69). MolNFT v1 #168776 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WQS
- Type
- protein
- Length
- 547 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
- Q8PMP0
- Ligands
- U7S, ZN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methionine--tRNA ligase (EC 6.1.1.10) | protein | 547 | 50% helix, 16% strand | Q8PMP0 |
Ligands and binding sites
- U7S · 2-{[3-({[4-bromo-5-(1-fluoroethenyl)-3-methylthiophen-2-yl]methyl}amino)propyl]amino}quinolin-4(1H)-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.69 | 0.78 | 64 | U7S |
| 2 | 67 | 0.31 | 0.75 | 24 | empty |
Compared structures
- 6WQS · Xanthomonas citri Methionyl-tRNA synthetase in complex with REP8839 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PMP0 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (Q8PMP0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8PMP0
- Elsewhere: RCSB PDB 6WQS · PDBe 6WQS · UniProt Q8PMP0
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