SMTL ID : 8sxn.1

Structure of NLRP3 and NEK7 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x 7YN: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea(Non-covalent)

7YN.1: 15 residues within 4Å: Chain C: A.101, A.102, R.225, I.285, L.287, V.288, T.313, Y.317, T.398, I.448, F.449, R.452, E.503, Y.506, D.536 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.285, C:L.287, C:V.288, C:T.313, C:F.449, C:F.449, C:Y.506, C:Y.506 Hydrogen bonds: C:A.102, C:A.102, C:R.225, C:R.452, C:R.452 7YN.3: 16 residues within 4Å: Chain D: A.101, A.102, R.225, I.285, L.287, V.288, T.313, Y.317, T.398, I.448, F.449, R.452, L.502, E.503, Y.506, D.536 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.285, D:L.287, D:V.288, D:T.313, D:F.449, D:F.449, D:L.502, D:Y.506, D:Y.506 Hydrogen bonds: D:A.102, D:A.102, D:R.452, D:R.452

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 17 residues within 4Å: Chain C: E.26, R.41, Y.42, T.43, L.45, G.103, G.105, K.106, T.107, I.108, E.180, F.247, Y.255, P.286, L.287, W.290, H.396 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.43, C:T.43, C:T.43, C:G.103, C:G.105, C:K.106, C:T.107, C:I.108, C:E.180, C:Y.255 Salt bridges: C:H.396, C:H.396 ATP.4: 17 residues within 4Å: Chain D: E.26, R.41, Y.42, T.43, L.45, G.103, G.105, K.106, T.107, I.108, E.180, F.247, Y.255, P.286, L.287, W.290, H.396 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:T.43, D:T.43, D:T.43, D:G.103, D:G.105, D:K.106, D:T.107, D:I.108, D:E.180, D:Y.255 Salt bridges: D:K.106, D:H.396, D:H.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Cryo-EM structures of NLRP3 reveal its self-activation mechanism. Nat Commun (2024)

Release Date

2024-02-14

Peptides

Serine/threonine-protein kinase Nek7: AB
NACHT, LRR and PYD domains-containing protein 3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Serine/threonine-protein kinase Nek7

NACHT, LRR and PYD domains-containing protein 3

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