SMTL ID : 7zgu.1

Human NLRP3-deltaPYD hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 residues within 4Å: Chain A: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.43, A:T.45, A:T.45, A:G.105, A:G.107, A:K.108, A:T.109, A:T.109, A:T.109, A:I.110, A:W.292 Salt bridges: A:K.108, A:H.398, A:H.398 pi-Stacking: A:F.249 ADP.2: 15 residues within 4Å: Chain B: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.43, B:T.45, B:T.45, B:G.105, B:G.107, B:K.108, B:T.109, B:T.109, B:T.109, B:I.110, B:W.292 Salt bridges: B:K.108, B:H.398, B:H.398 pi-Stacking: B:F.249 ADP.3: 15 residues within 4Å: Chain C: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.43, C:T.45, C:T.45, C:G.105, C:G.107, C:K.108, C:T.109, C:T.109, C:T.109, C:I.110, C:W.292 Salt bridges: C:K.108, C:H.398, C:H.398 pi-Stacking: C:F.249 ADP.4: 15 residues within 4Å: Chain D: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.43, D:T.45, D:T.45, D:G.105, D:G.107, D:K.108, D:T.109, D:T.109, D:T.109, D:I.110, D:W.292 Salt bridges: D:K.108, D:H.398, D:H.398 pi-Stacking: D:F.249 ADP.5: 15 residues within 4Å: Chain E: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:R.43, E:T.45, E:T.45, E:G.105, E:G.107, E:K.108, E:T.109, E:T.109, E:T.109, E:I.110, E:W.292 Salt bridges: E:K.108, E:H.398, E:H.398 pi-Stacking: E:F.249 ADP.6: 15 residues within 4Å: Chain F: R.43, Y.44, T.45, L.47, A.104, G.105, G.107, K.108, T.109, I.110, F.249, Y.257, P.288, W.292, H.398 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.43, F:T.45, F:T.45, F:G.105, F:G.107, F:K.108, F:T.109, F:T.109, F:T.109, F:I.110, F:W.292 Salt bridges: F:K.108, F:H.398, F:H.398 pi-Stacking: F:F.249

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raisch, T. et al., Cryo-EM structure of the NEK7-independent NLRP3 inflammasome. To Be Published

Release Date

2022-05-18

Peptides

NACHT, LRR and PYD domains-containing protein 3: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NACHT, LRR and PYD domains-containing protein 3