MolNFT v1 · #125394 · protein
In silico-powered specific incorporation of photocaged dopa at multiple protein sites
5L7P · Tyrosine--tRNA ligase: “In silico-powered specific incorporation of photocaged dopa at multiple protein sites”. X-ray diffraction, 3 ligands (BUU, CA, CL), 3 pockets (best druggability 0.79). MolNFT v1 #125394 on GenesisL1: 3D…
- PDB
- 5L7P
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase
- EC
- 6.1.1.1
- UniProt
- Q57834
- Ligands
- BUU, CA, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 301 | 51% helix, 14% strand | Q57834 |
| B | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 306 | 49% helix, 13% strand | Q57834 |
Ligands and binding sites
- BUU · (2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid · ligand · chains B
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.79 | 0.86 | 58 | BUU |
| 2 | 583 | 0.72 | 0.80 | 54 | 1PE, CL |
| 3 | 823 | 0.69 | 0.75 | 76 | empty |
Interfaces
1 interface between chains.
- A–B · 248 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5L7P · In silico-powered specific incorporation of photocaged Dopa at multiple protein sites · the same entry in another collection · chain A against A, TM-score 1.00
- Q57834 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q57834) · a predicted model of the same protein · chain B 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 Q57834
- Elsewhere: RCSB PDB 5L7P · PDBe 5L7P · UniProt Q57834
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