Research workbench
Cryo-EM structure of the NLRP1-card filament
Analyse Cryo-EM structure of the NLRP1-card filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XKK
- Type
- protein
- Length
- 3,740 residues
- Chains
- 44
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nacht, lrr and pyd domains-containing protein 1
- UniProt
- Q9C000
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v | Nacht, lrr and pyd domains-containing protein 1 | protein | 85 | 72% helix, 2% strand | Q9C000 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.80 | 0.81 | 113 | empty |
| 2 | 730 | 0.77 | 0.81 | 81 | empty |
| 3 | 697 | 0.76 | 0.81 | 72 | empty |
| 4 | 670 | 0.76 | 0.82 | 71 | empty |
| 5 | 643 | 0.75 | 0.81 | 73 | empty |
Interfaces
81 interfaces between chains.
- H–I · 476 Ų buried · 10 hydrogen bonds · protein-protein
- E–J · 476 Ų buried · 10 hydrogen bonds · protein-protein
- O–P · 468 Ų buried · 10 hydrogen bonds · protein-protein
- G–O · 467 Ų buried · 10 hydrogen bonds · protein-protein
- M–R · 467 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6XKK · Cryo-EM structure of the NLRP1-CARD filament · the same entry in another collection · chain u against u, TM-score 1.00
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 6XKK · PDBe 6XKK · UniProt Q9C000
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