MolNFT v1 · #103275 · protein
Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to 4-trans-cyclooctene-amidopheylalanine (tco-amf)
4PBT · Tyrosine--tRNA ligase: “Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to…”. X-ray diffraction, 2 ligands (P4G, 2LQ), 1 pocket (best druggability 0.79). MolNFT v1 #103275 on GenesisL1: 3D structure, binding…
- PDB
- 4PBT
- Type
- protein
- Length
- 310 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine--tRNA ligase
- EC
- 6.1.1.1
- UniProt
- Q57834
- Ligands
- P4G, 2LQ
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine--tRNA ligase (EC 6.1.1.1) | protein | 310 | 51% helix, 13% strand | Q57834 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains A
- 2LQ · 4-{[(1R,4E)-cyclooct-4-en-1-ylcarbonyl]amino}-L-phenylalanine · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.79 | 0.85 | 57 | GOL, 2LQ |
Compared structures
- 4PBT · Crystal structure of the M. jannaschii G2 tRNA synthetase variant bound to… · 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 A 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 Q57834
- Elsewhere: RCSB PDB 4PBT · PDBe 4PBT · UniProt Q57834
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