Research workbench
Catalytic domain of pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with an adenylated furan-bearing noncanonical amino acid and pyrophosphate
Analyse Catalytic domain of pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CS3
- Type
- protein
- Length
- 270 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
- LYS, AMP, FU0, POP, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysine--tRNA ligase (EC 6.1.1.26) | protein | 270 | 37% helix, 24% strand | Q8PWY1 |
Ligands and binding sites
- LYS · Lysine · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A
- FU0 · 2-(furan-2-yl)ethyl hydrogen carbonate · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.78 | 0.87 | 49 | LYS, AMP, FU0, POP, MG |
| 2 | 61 | 0.34 | 0.77 | 14 | empty |
| 3 | 61 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 4CS3 · Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with an… · 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 4CS3 · PDBe 4CS3 · UniProt Q8PWY1
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