MolNFT v1 · #87982 · protein
Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl lysine
4CH6 · Pyrrolysine--tRNA ligase: “Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl lysine”. X-ray diffraction, 2 ligands (YLA, MG), 2 pockets (best druggability 0.66). MolNFT v1 #87982 on GenesisL1…
- PDB
- 4CH6
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysine--tRNA ligase
- EC
- 6.1.1.26
- UniProt
- Q8PWY1
- Ligands
- YLA, MG
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 263 | 38% helix, 22% strand | Q8PWY1 |
Ligands and binding sites
- YLA · (S)-2-amino-6-(((prop-2-yn-1-yloxy)carbonyl)amino)hexanoic (((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric)anhydride · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.66 | 0.80 | 42 | YLA, MG |
| 2 | 70 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 4CH6 · Structure of pyrrolysyl-tRNA synthetase in complex with adenylated propargyloxycarbonyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PWY1 · AlphaFold monomer V2.0 prediction for pyrrolysine--tRNA ligase (Q8PWY1) · 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 Q8PWY1
- Elsewhere: RCSB PDB 4CH6 · PDBe 4CH6 · UniProt Q8PWY1
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