MolNFT v1 · #57513 · protein
Crystal structure of rat selenocysteine lyase
3A9X: “Crystal structure of rat selenocysteine lyase”. X-ray diffraction, 2 ligands (PLP, PO4), 10 pockets (best druggability 0.81). MolNFT v1 #57513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A9X
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine lyase
- EC
- 4.4.1.16
- UniProt
- Q68FT9
- Ligands
- PLP, PO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine lyase (EC 4.4.1.16) | protein | 388 | 46% helix, 16% strand | Q68FT9 |
| B | Selenocysteine lyase (EC 4.4.1.16) | protein | 400 | 48% helix, 15% strand | Q68FT9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.81 | 0.87 | 105 | PLP, PO4 |
| 2 | 524 | 0.75 | 0.82 | 30 | empty |
| 3 | 258 | 0.60 | 0.80 | 42 | empty |
| 4 | 147 | 0.48 | 0.78 | 24 | empty |
| 5 | 53 | 0.46 | 0.85 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2035 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 Q68FT9
- Elsewhere: RCSB PDB 3A9X · PDBe 3A9X · UniProt Q68FT9
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