MolNFT v1 · #74565 · protein
Leishmania major tyrosyl-tRNA synthetase in complex with tyrosinol, triclinic crystal form 1
3P0J: “Leishmania major tyrosyl-tRNA synthetase in complex with tyrosinol, triclinic crystal form 1”. X-ray diffraction, 2 ligands (TYE, NA), 20 pockets (best druggability 0.80). MolNFT v1 #74565 on GenesisL1: 3D structure, binding sites…
- PDB
- 3P0J
- Type
- protein
- Length
- 2,566 residues
- Chains
- 4
- 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, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 657 | 52% helix, 11% strand | Q4QFJ7 |
| B | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 581 | 53% helix, 9% strand | Q4QFJ7 |
| C | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 663 | 51% helix, 10% strand | Q4QFJ7 |
| D | Tyrosyl-tRNA synthetase (EC 6.1.1.1) | protein | 665 | 53% helix, 9% strand | Q4QFJ7 |
Ligands and binding sites
- TYE · 4-[(2S)-2-amino-3-hydroxypropyl]phenol · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.80 | 0.87 | 58 | TYE |
| 2 | 428 | 0.75 | 0.84 | 53 | TYE |
| 3 | 513 | 0.74 | 0.82 | 53 | TYE |
| 4 | 570 | 0.72 | 0.80 | 62 | TYE |
| 5 | 342 | 0.62 | 0.78 | 54 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1218 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1188 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 229 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3P0J · Leishmania major Tyrosyl-tRNA synthetase in complex with tyrosinol, triclinic crystal… · the same entry in another collection · chain D against D, 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 3P0J · PDBe 3P0J · UniProt Q4QFJ7
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