Research workbench
Catalytic domain of pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with amppnp
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
- 4CS4
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrrolysyl-tRNA synthetase
- EC
- 6.1.1.26
- UniProt
- Q8PWY1
- Ligands
- ANP, AXZ, MG, PO4
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrrolysyl-tRNA synthetase (EC 6.1.1.26) | protein | 268 | 38% helix, 24% strand | Q8PWY1 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- AXZ · 2-{[dihydroxy(4-aminoethylphenyl)-{4}-sulfanyl]amino}-3-hydroxypropanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 20 copies · 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 | 443 | 0.78 | 0.86 | 54 | ANP, EDO, MG, AXZ |
| 2 | 134 | 0.43 | 0.76 | 18 | empty |
| 3 | 56 | 0.32 | 0.76 | 13 | empty |
Compared structures
- 4CS4 · Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with AMPPNP · 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 4CS4 · PDBe 4CS4 · UniProt Q8PWY1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.