SMTL ID : 7pzc.1

Cryo-EM structure of the NLRP3 decamer bound to the inhibitor CRID3

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.168, A:T.169, A:G.229, A:I.230, A:G.231, A:K.232, A:T.233, A:T.233, A:T.233, A:I.234 Salt bridges: A:K.232, A:H.522, A:H.522 ADP.3: 16 residues within 4Å: Chain B: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.168, B:T.169, B:G.229, B:I.230, B:G.231, B:K.232, B:T.233, B:T.233, B:T.233, B:I.234 Salt bridges: B:K.232, B:H.522, B:H.522 ADP.5: 16 residues within 4Å: Chain C: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.168, C:T.169, C:G.229, C:I.230, C:G.231, C:K.232, C:T.233, C:T.233, C:T.233, C:I.234 Salt bridges: C:K.232, C:H.522, C:H.522 ADP.7: 16 residues within 4Å: Chain D: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.168, D:T.169, D:G.229, D:I.230, D:G.231, D:K.232, D:T.233, D:T.233, D:T.233, D:I.234 Salt bridges: D:K.232, D:H.522, D:H.522 ADP.9: 16 residues within 4Å: Chain E: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.168, E:T.169, E:G.229, E:I.230, E:G.231, E:K.232, E:T.233, E:T.233, E:T.233, E:I.234 Salt bridges: E:K.232, E:H.522, E:H.522 ADP.11: 16 residues within 4Å: Chain F: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.168, F:T.169, F:G.229, F:I.230, F:G.231, F:K.232, F:T.233, F:T.233, F:T.233, F:I.234 Salt bridges: F:K.232, F:H.522, F:H.522 ADP.13: 16 residues within 4Å: Chain G: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:Y.168, G:T.169, G:G.229, G:I.230, G:G.231, G:K.232, G:T.233, G:T.233, G:T.233, G:I.234 Salt bridges: G:K.232, G:H.522, G:H.522 ADP.15: 16 residues within 4Å: Chain H: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Y.168, H:T.169, H:G.229, H:I.230, H:G.231, H:K.232, H:T.233, H:T.233, H:T.233, H:I.234 Salt bridges: H:K.232, H:H.522, H:H.522 ADP.17: 16 residues within 4Å: Chain I: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:Y.168, I:T.169, I:G.229, I:I.230, I:G.231, I:K.232, I:T.233, I:T.233, I:T.233, I:I.234 Salt bridges: I:K.232, I:H.522, I:H.522 ADP.19: 16 residues within 4Å: Chain J: R.167, Y.168, T.169, A.227, A.228, G.229, I.230, G.231, K.232, T.233, I.234, F.373, Y.381, L.413, W.416, H.522 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:Y.168, J:T.169, J:G.229, J:I.230, J:G.231, J:K.232, J:T.233, J:T.233, J:T.233, J:I.234 Salt bridges: J:K.232, J:H.522, J:H.522

10 x 8GI: 1-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)-3-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-urea(Non-covalent)

8GI.2: 15 residues within 4Å: Chain A: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.411, A:V.414, A:T.439, A:F.575, A:L.628, A:Y.632 Hydrogen bonds: A:A.228, A:A.228, A:A.228, A:R.351, A:R.578, A:R.578 pi-Cation interactions: A:R.578 8GI.4: 15 residues within 4Å: Chain B: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.411, B:V.414, B:T.439, B:F.575, B:L.628, B:Y.632 Hydrogen bonds: B:A.228, B:A.228, B:A.228, B:R.351, B:R.578, B:R.578 pi-Cation interactions: B:R.578 8GI.6: 15 residues within 4Å: Chain C: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.411, C:V.414, C:T.439, C:F.575, C:L.628, C:Y.632 Hydrogen bonds: C:A.228, C:A.228, C:A.228, C:R.351, C:R.578, C:R.578 pi-Cation interactions: C:R.578 8GI.8: 15 residues within 4Å: Chain D: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:I.411, D:V.414, D:T.439, D:F.575, D:L.628, D:Y.632 Hydrogen bonds: D:A.228, D:A.228, D:A.228, D:R.351, D:R.578, D:R.578 pi-Cation interactions: D:R.578 8GI.10: 15 residues within 4Å: Chain E: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:I.411, E:V.414, E:T.439, E:F.575, E:L.628, E:Y.632 Hydrogen bonds: E:A.228, E:A.228, E:A.228, E:R.351, E:R.578, E:R.578 pi-Cation interactions: E:R.578 8GI.12: 15 residues within 4Å: Chain F: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:I.411, F:V.414, F:T.439, F:F.575, F:L.628, F:Y.632 Hydrogen bonds: F:A.228, F:A.228, F:A.228, F:R.351, F:R.578, F:R.578 pi-Cation interactions: F:R.578 8GI.14: 15 residues within 4Å: Chain G: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:I.411, G:V.414, G:T.439, G:F.575, G:L.628, G:Y.632 Hydrogen bonds: G:A.228, G:A.228, G:A.228, G:R.351, G:R.578, G:R.578 pi-Cation interactions: G:R.578 8GI.16: 15 residues within 4Å: Chain H: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:I.411, H:V.414, H:T.439, H:F.575, H:L.628, H:Y.632 Hydrogen bonds: H:A.228, H:A.228, H:A.228, H:R.351, H:R.578, H:R.578 pi-Cation interactions: H:R.578 8GI.18: 15 residues within 4Å: Chain I: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:I.411, I:V.414, I:T.439, I:F.575, I:L.628, I:Y.632 Hydrogen bonds: I:A.228, I:A.228, I:A.228, I:R.351, I:R.578, I:R.578 pi-Cation interactions: I:R.578 8GI.20: 15 residues within 4Å: Chain J: A.227, A.228, R.351, M.408, I.411, V.414, T.439, Y.443, I.574, F.575, R.578, L.628, E.629, Y.632, M.661 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:I.411, J:V.414, J:T.439, J:F.575, J:L.628, J:Y.632 Hydrogen bonds: J:A.228, J:A.228, J:A.228, J:R.351, J:R.578, J:R.578 pi-Cation interactions: J:R.578

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hochheiser, I.V. et al., Structure of the NLRP3 decamer bound to the cytokine release inhibitor CRID3. Nature (2022)

Release Date

2022-01-26

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

NACHT, LRR and PYD domains-containing protein 3