Research workbench
Leishmania major tyrosyl-tRNA synthetase in complex with tyrosinol, cubic crystal form
Analyse Leishmania major tyrosyl-tRNA synthetase in complex with tyrosinol, cubic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P0I
- Type
- protein
- Length
- 1,209 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
- TYE
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 673 | 51% helix, 10% strand | Q4QFJ7 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 536 | 52% helix, 11% strand | Q4QFJ7 |
Ligands and binding sites
- TYE · 4-[(2S)-2-amino-3-hydroxypropyl]phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.76 | 0.82 | 74 | TYE |
| 2 | 544 | 0.76 | 0.83 | 59 | TYE |
| 3 | 786 | 0.69 | 0.76 | 84 | empty |
| 4 | 600 | 0.66 | 0.76 | 61 | empty |
| 5 | 108 | 0.52 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1068 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 modified (engineered).
Compared structures
- 3P0I · Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, 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 3P0I · PDBe 3P0I · UniProt Q4QFJ7
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