Research workbench
Independent saturation of three trprs subsites generates a partially- assembled state similar to those observed in molecular simulations
Analyse Independent saturation of three trprs subsites generates a partially- assembled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FHJ
- Type
- protein
- Length
- 1,743 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophanyl-tRNA synthetase
- EC
- 6.1.1.2
- UniProt
- P00953
- Ligands
- TRP, AMP, PO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 299 | 58% helix, 8% strand | P00953 |
| D | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 286 | 55% helix, 9% strand | P00953 |
| B | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 291 | 59% helix, 7% strand | P00953 |
| C | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 279 | 59% helix, 8% strand | P00953 |
| E | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 292 | 60% helix, 8% strand | P00953 |
| F | Tryptophanyl-tRNA synthetase (EC 6.1.1.2) | protein | 296 | 59% helix, 9% strand | P00953 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 6 copies · chains A, D, B, C, E, F
- AMP · Adenosine monophosphate · ligand · 6 copies · chains A, D, B, C, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.76 | 0.79 | 78 | TRP, PO4, AMP |
| 2 | 1111 | 0.74 | 0.77 | 93 | TRP, PO4, AMP |
| 3 | 814 | 0.74 | 0.78 | 60 | TRP, PO4, AMP |
| 4 | 1109 | 0.73 | 0.76 | 92 | TRP, PO4, AMP |
| 5 | 711 | 0.73 | 0.79 | 55 | TRP, PO4, AMP |
Interfaces
8 interfaces between chains.
- A–B · 2165 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2144 Ų buried · 38 hydrogen bonds · protein-protein
- D–C · 2075 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 363 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FHJ · Independent saturation of three TrpRS subsites generates a partially-assembled state… · the same entry in another collection · chain B against B, TM-score 1.00
- P00953 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (P00953) · a predicted model of the same protein · chain F 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 P00953
- Elsewhere: RCSB PDB 3FHJ · PDBe 3FHJ · UniProt P00953
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