MolNFT v1 · #158306 · protein

Cryo-EM structure of NLRP3 bound to NEK7

6NPY · Nacht, lrr and pyd domains-containing protein 3: “Cryo-EM structure of NLRP3 bound to NEK7”. Electron microscopy, 1 ligand (ADP), 18 pockets (best druggability 0.88). MolNFT v1 #158306 on GenesisL1: 3D structure, binding sites and…

PDB: 6NPY
Type: protein
Length: 965 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nacht, lrr and pyd domains-containing protein 3; Protein kinase…
EC: 2.7.11.1
UniProt: Q96P20, P19525, Q8TDX7
Ligands: ADP
Pockets: 18 · best druggability 0.88

Structure

electron microscopy · 2 distinct chains · 41% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nacht, lrr and pyd domains-containing protein 3	protein	798	38% helix, 8% strand	Q96P20
B	Protein kinase R,SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1)	protein	167	54% helix, 3% strand	P19525, Q8TDX7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	806	0.88	0.90	101	empty
2	1008	0.84	0.85	111	empty
3	512	0.82	0.89	59	ADP
4	150	0.80	0.96	42	empty
5	165	0.80	0.95	46	empty

Interfaces

1 interface between chains.

A–B · 1792 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6NPY · Cryo-EM structure of NLRP3 bound to NEK7 · the same entry in another collection · chain A against A, TM-score 1.00
Q8TDX7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK7 (Q8TDX7) · a predicted model of the same protein · chain B against A, TM-score 0.94
P19525 · AlphaFold monomer V2.0 prediction for interferon-induced, double- stranded RNA-activated… · a predicted model of the same protein · chain B against A, TM-score 0.78
Q96P20 · AlphaFold monomer V2.0 prediction for nacht, lrr and pyd domains- containing protein 3… · a predicted model of the same protein · chain A against A, TM-score 0.64

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
Every structure of UniProt P19525
Every structure of UniProt Q8TDX7
Elsewhere: RCSB PDB 6NPY · PDBe 6NPY · UniProt Q96P20 · UniProt P19525 · UniProt Q8TDX7

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