MolNFT v1 · #172223 · protein
Crystal structure of unliganded mlkl executioner domain
6ZVO · Mixed lineage kinase domain-like protein: “Crystal structure of unliganded mlkl executioner domain”. X-ray diffraction, 2 ligands (CL, BR), 4 pockets (best druggability 0.77). MolNFT v1 #172223 on GenesisL1: 3D structure, binding…
- PDB
- 6ZVO
- Type
- protein
- Length
- 429 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mixed lineage kinase domain-like protein
- UniProt
- Q8NB16
- Ligands
- CL, BR
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mixed lineage kinase domain-like protein | protein | 145 | 78% helix, 0% strand | Q8NB16 |
| B | Mixed lineage kinase domain-like protein | protein | 144 | 79% helix, 0% strand | Q8NB16 |
| C | Mixed lineage kinase domain-like protein | protein | 140 | 79% helix, 0% strand | Q8NB16 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.77 | 0.79 | 81 | CL |
| 2 | 855 | 0.76 | 0.79 | 73 | empty |
| 3 | 116 | 0.46 | 0.78 | 15 | empty |
| 4 | 93 | 0.45 | 0.79 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 498 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6ZVO · Crystal structure of unliganded MLKL executioner domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NB16 · AlphaFold monomer V2.0 prediction for mixed lineage kinase domain- like protein (Q8NB16) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q8NB16
- Elsewhere: RCSB PDB 6ZVO · PDBe 6ZVO · UniProt Q8NB16
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