MolNFT v1 · #140223 · protein
Crystal structure of human NLRP1 leucine rich repeat domain
5Y3S · Nacht, lrr and pyd domains-containing protein 1: “Crystal structure of human NLRP1 leucine rich repeat domain”. X-ray diffraction, 2 ligands (NA, PO4), 5 pockets (best druggability 0.68). MolNFT v1 #140223 on GenesisL1: 3D…
- PDB
- 5Y3S
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nacht, lrr and pyd domains-containing protein 1
- UniProt
- Q9C000
- Ligands
- NA, PO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nacht, lrr and pyd domains-containing protein 1 | protein | 198 | 40% helix, 12% strand | Q9C000 |
| B | Nacht, lrr and pyd domains-containing protein 1 | protein | 198 | 42% helix, 12% strand | Q9C000 |
| C | Nacht, lrr and pyd domains-containing protein 1 | protein | 201 | 42% helix, 10% strand | Q9C000 |
| D | Nacht, lrr and pyd domains-containing protein 1 | protein | 199 | 42% helix, 12% strand | Q9C000 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.68 | 0.83 | 44 | empty |
| 2 | 471 | 0.66 | 0.78 | 52 | PO4 |
| 3 | 191 | 0.46 | 0.75 | 33 | empty |
| 4 | 56 | 0.46 | 0.84 | 11 | empty |
| 5 | 81 | 0.29 | 0.72 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 743 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 679 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 620 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 291 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5Y3S · Crystal structure of human NLRP1 leucine rich repeat domain · the same entry in another collection · chain D against D, TM-score 1.00
- Q9C000 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 1… · a predicted model of the same protein · chain D 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 Q9C000
- Elsewhere: RCSB PDB 5Y3S · PDBe 5Y3S · UniProt Q9C000
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