MolNFT v1 · #168777 · protein
Xanthomonas citri methionyl-tRNA synthetase in complex with REP3123
6WQT · Methionine--tRNA ligase: “Xanthomonas citri methionyl-tRNA synthetase in complex with REP3123”. X-ray diffraction, 2 ligands (U81, ZN), 2 pockets (best druggability 0.68). MolNFT v1 #168777 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WQT
- 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
- U81, ZN
- Pockets
- 2 · best druggability 0.68
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
- U81 · 5-[(3-{[(4R)-6,8-dibromo-3,4-dihydro-2H-1-benzopyran-4-yl]amino}propyl)amino]thieno[3,2-b]pyridin-7(6H)-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 | 543 | 0.68 | 0.78 | 65 | U81 |
| 2 | 51 | 0.30 | 0.76 | 9 | empty |
Compared structures
- 6WQT · Xanthomonas citri Methionyl-tRNA synthetase in complex with REP3123 · 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 0.99
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 Q8PMP0
- Elsewhere: RCSB PDB 6WQT · PDBe 6WQT · UniProt Q8PMP0
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