MolNFT v1 · #65519 · protein
Structure of human selenocysteine lyase
3GZC: “Structure of human selenocysteine lyase”. X-ray diffraction, 1 ligand (PLR), 12 pockets (best druggability 0.82). MolNFT v1 #65519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GZC
- Type
- protein
- Length
- 805 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine lyase
- EC
- 4.4.1.16
- UniProt
- Q96I15
- Ligands
- PLR
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | Q96I15 |
| B | Selenocysteine lyase (EC 4.4.1.16) | protein | 402 | 44% helix, 16% strand | Q96I15 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.82 | 0.85 | 128 | PLR |
| 2 | 432 | 0.75 | 0.84 | 35 | empty |
| 3 | 93 | 0.42 | 0.79 | 24 | empty |
| 4 | 94 | 0.42 | 0.78 | 26 | empty |
| 5 | 54 | 0.41 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2191 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 Q96I15
- Elsewhere: RCSB PDB 3GZC · PDBe 3GZC · UniProt Q96I15
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