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Cryo-EM structure of the NLRP3 pyd filament

Analyse Cryo-EM structure of the NLRP3 pyd filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PZD
Type: protein
Length: 1,656 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nacht, lrr and pyd domains-containing protein 3
UniProt: Q96P20
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 1 distinct chain · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	Nacht, lrr and pyd domains-containing protein 3	protein	92	65% helix, 0% strand	Q96P20

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	876	0.74	0.79	73	empty
2	495	0.67	0.78	49	empty
3	447	0.67	0.79	50	empty
4	536	0.66	0.77	57	empty
5	455	0.66	0.78	38	empty

Interfaces

42 interfaces between chains.

P–S · 542 Å² buried · 7 hydrogen bonds · protein-protein
K–N · 542 Å² buried · 7 hydrogen bonds · protein-protein
N–Q · 541 Å² buried · 7 hydrogen bonds · protein-protein
S–V · 540 Å² buried · 7 hydrogen bonds · protein-protein
Q–T · 540 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7PZD · Cryo-EM structure of the NLRP3 PYD filament · the same entry in another collection · chain X against X, 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 Q96P20
Elsewhere: RCSB PDB 7PZD · PDBe 7PZD · UniProt Q96P20

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