MolNFT v1 · #191035 · protein

Human NLRP3-deltapyd hexamer

7ZGU · Nacht, lrr and pyd domains-containing protein 3: “Human NLRP3-deltapyd hexamer”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.85). MolNFT v1 #191035 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7ZGU
Type: protein
Length: 4,854 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nacht, lrr and pyd domains-containing protein 3
UniProt: Q96P20
Ligands: ADP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 46% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nacht, lrr and pyd domains-containing protein 3	protein	809	46% helix, 10% strand	Q96P20

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

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	1125	0.85	0.86	117	ADP
2	1108	0.85	0.86	112	ADP
3	1076	0.85	0.85	114	ADP
4	1101	0.84	0.85	116	ADP
5	1090	0.84	0.85	114	ADP

Interfaces

9 interfaces between chains.

D–F · 550 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 546 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 536 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 535 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 534 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7ZGU · Human NLRP3-deltaPYD hexamer · the same entry in another collection · chain C against C, TM-score 1.00
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 0.67

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 7ZGU · PDBe 7ZGU · UniProt Q96P20

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