MolNFT v1 · #123997 · protein
Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant Y306A/N346A/C348A/Y384F in complex with amppnp
5K1X · Pyrrolysine--tRNA ligase: “Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant Y306A/N346A/C348A/Y384F in complex with…”. X-ray diffraction, 3 ligands (ANP, MG, CL), 2 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5K1X
- Type
- protein
- Length
- 268 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
- ANP, MG, CL
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 268 | 38% helix, 25% strand | Q8PWY1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 480 | 0.80 | 0.87 | 53 | ANP, MG, PEG, CL |
| 2 | 90 | 0.37 | 0.76 | 17 | empty |
Compared structures
- 5K1X · Catalytic domain of polyspecific pyrrolysyl-tRNA synthetase mutant… · 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 0.99
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 Q8PWY1
- Elsewhere: RCSB PDB 5K1X · PDBe 5K1X · UniProt Q8PWY1
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