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Cryo-EM structure of NLRP6 pyd filament

Analyse Cryo-EM structure of NLRP6 pyd filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NCV
Type: protein
Length: 1,911 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nacht, lrr and pyd domains-containing protein 6
UniProt: P59044
Pockets: 20 · best druggability 0.66

Structure

electron microscopy · 1 distinct chain · 57% helix, 0% 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, V	Nacht, lrr and pyd domains-containing protein 6	protein	91	57% helix, 0% strand	P59044

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	377	0.66	0.80	38	empty
2	372	0.66	0.80	38	empty
3	386	0.66	0.79	38	empty
4	380	0.65	0.80	41	empty
5	360	0.65	0.80	38	empty

Interfaces

51 interfaces between chains.

E–F · 474 Å² buried · 3 hydrogen bonds · protein-protein
T–V · 472 Å² buried · 3 hydrogen bonds · protein-protein
Q–R · 471 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 470 Å² buried · 3 hydrogen bonds · protein-protein
L–M · 470 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6NCV · Cryo-EM structure of NLRP6 PYD filament · the same entry in another collection · chain V against V, 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 P59044
Elsewhere: RCSB PDB 6NCV · PDBe 6NCV · UniProt P59044

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