MolNFT v1 · #57515 · protein
Crystal structure of RAS selenocysteine lyase in complex with selenopropionate
3A9Z: “Crystal structure of RAS selenocysteine lyase in complex with selenopropionate”. X-ray diffraction, 3 ligands (PLP, SLP, PO4), 11 pockets (best druggability 0.88). MolNFT v1 #57515 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3A9Z
- Type
- protein
- Length
- 802 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, SLP, PO4
- Pockets
- 11 · best druggability 0.88
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 | 403 | 47% helix, 15% strand | Q68FT9 |
| B | Selenocysteine lyase (EC 4.4.1.16) | protein | 399 | 46% helix, 16% strand | Q68FT9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SLP · 3-selanylpropanoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.88 | 0.97 | 82 | PLP, SLP |
| 2 | 491 | 0.74 | 0.82 | 30 | empty |
| 3 | 158 | 0.52 | 0.80 | 42 | empty |
| 4 | 108 | 0.48 | 0.81 | 32 | empty |
| 5 | 56 | 0.47 | 0.85 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2288 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3A9Z · Crystal structure of ras selenocysteine lyase in complex with selenopropionate · the same entry in another collection · chain A against A, TM-score 1.00
- Q68FT9 · AlphaFold monomer V2.0 prediction for selenocysteine lyase (Q68FT9) · a predicted model of the same protein · chain B 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 Q68FT9
- Elsewhere: RCSB PDB 3A9Z · PDBe 3A9Z · UniProt Q68FT9
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