SMTL ID : 8xji.1

Structure of chimeric RyR complex with flubendiamide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x 01: Flubendiamide

01.1: 13 residues within 4Å: Chain I: K.4563, Y.4564, A.4566, L.4567, S.4788, Y.4791, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820, R.4824 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:K.4563, I:K.4563, I:Y.4564, I:A.4566, I:L.4567, I:Y.4791, I:Y.4795, I:M.4818 Hydrogen bonds: I:K.4563, I:D.4815, I:D.4815 Halogen bonds: I:Y.4564, I:Y.4564, I:G.4819 01.6: 13 residues within 4Å: Chain J: K.4563, Y.4564, A.4566, L.4567, S.4788, Y.4791, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820, R.4824 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:K.4563, J:K.4563, J:Y.4564, J:A.4566, J:L.4567, J:Y.4791, J:Y.4795, J:M.4818 Hydrogen bonds: J:K.4563, J:D.4815, J:D.4815 Halogen bonds: J:Y.4564, J:Y.4564, J:G.4819 01.11: 13 residues within 4Å: Chain K: K.4563, Y.4564, A.4566, L.4567, S.4788, Y.4791, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820, R.4824 14 PLIP interactions: 14 interactions with chain K Hydrophobic interactions: K:K.4563, K:K.4563, K:Y.4564, K:A.4566, K:L.4567, K:Y.4791, K:Y.4795, K:M.4818 Hydrogen bonds: K:K.4563, K:D.4815, K:D.4815 Halogen bonds: K:Y.4564, K:Y.4564, K:G.4819 01.16: 13 residues within 4Å: Chain L: K.4563, Y.4564, A.4566, L.4567, S.4788, Y.4791, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820, R.4824 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:K.4563, L:K.4563, L:Y.4564, L:A.4566, L:L.4567, L:Y.4791, L:Y.4795, L:M.4818 Hydrogen bonds: L:K.4563, L:D.4815, L:D.4815 Halogen bonds: L:Y.4564, L:Y.4564, L:G.4819

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain I: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.4958, I:C.4961, I:H.4978, I:H.4983 ZN.7: 5 residues within 4Å: Chain J: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4958, J:C.4961, J:H.4978, J:H.4983 ZN.12: 5 residues within 4Å: Chain K: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4958, K:C.4961, K:H.4978, K:H.4983 ZN.17: 5 residues within 4Å: Chain L: C.4958, C.4961, H.4978, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.4958, L:C.4961, L:H.4978, L:H.4983

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain I: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:E.3893, I:E.3967, I:T.5001 CA.8: 5 residues within 4Å: Chain J: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.3893, J:E.3967, J:T.5001 CA.13: 5 residues within 4Å: Chain K: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:E.3893, K:E.3967, K:T.5001 CA.18: 5 residues within 4Å: Chain L: E.3893, H.3895, E.3967, Q.3970, T.5001 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:E.3893, L:E.3967, L:T.5001

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

ATP.4: 6 residues within 4Å: Chain I: M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:H.4983 Salt bridges: I:K.4214 ATP.9: 6 residues within 4Å: Chain J: M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:H.4983 Salt bridges: J:K.4214 ATP.14: 6 residues within 4Å: Chain K: M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:H.4983 Salt bridges: K:K.4214 ATP.19: 6 residues within 4Å: Chain L: M.4954, K.4957, C.4958, T.4979, H.4983, L.4985 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:H.4983 Salt bridges: L:K.4214

4 x CFF: CAFFEINE(Non-covalent)

CFF.5: 6 residues within 4Å: Chain I: F.3753, E.4239, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain I pi-Stacking: I:W.4716, I:W.4716, I:W.4716, I:W.4716 CFF.10: 6 residues within 4Å: Chain J: F.3753, E.4239, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain J pi-Stacking: J:W.4716, J:W.4716, J:W.4716, J:W.4716 CFF.15: 6 residues within 4Å: Chain K: F.3753, E.4239, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain K pi-Stacking: K:W.4716, K:W.4716, K:W.4716, K:W.4716 CFF.20: 6 residues within 4Å: Chain L: F.3753, E.4239, I.4242, W.4716, I.4996, Y.5014 4 PLIP interactions: 4 interactions with chain L pi-Stacking: L:W.4716, L:W.4716, L:W.4716, L:W.4716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, L. et al., Cryo-EM structures of ryanodine receptors and diamide insecticides reveal the mechanisms of selectivity and resistance. Nat Commun (2024)

Release Date

2024-10-30

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ACEG
Calmodulin-1: BDFH
Ryanodine receptor 1: IJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
G

E
F

G
E

B
L

D
K

F
J

H
I

I
D

J
A

K
B

L
C

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

Ryanodine receptor 1

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