MolNFT v1 · #74563 · protein
Leishmania major tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form
3P0H: “Leishmania major tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form”. X-ray diffraction, 1 ligand (FSE), 17 pockets (best druggability 0.73). MolNFT v1 #74563 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3P0H
- Type
- protein
- Length
- 1,263 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-tRNA synthetase
- EC
- 6.1.1.1
- UniProt
- Q4QFJ7
- Ligands
- FSE
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 665 | 52% helix, 11% strand | Q4QFJ7 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 598 | 53% helix, 11% strand | Q4QFJ7 |
Ligands and binding sites
- FSE · 3,7,3',4'-tetrahydroxyflavone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.73 | 0.79 | 65 | FSE |
| 2 | 673 | 0.73 | 0.79 | 65 | FSE |
| 3 | 687 | 0.68 | 0.76 | 59 | empty |
| 4 | 672 | 0.68 | 0.77 | 60 | empty |
| 5 | 199 | 0.59 | 0.81 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1129 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 3P0H · Leishmania major Tyrosyl-tRNA synthetase in complex with fisetin, cubic crystal form · 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 Q4QFJ7
- Elsewhere: RCSB PDB 3P0H · PDBe 3P0H · UniProt Q4QFJ7
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