SMTL ID : 6m2w.1

Structure of RyR1 (Ca2+/Caffeine/ATP/CaM1234/CHL)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x CFF: CAFFEINE(Non-covalent)

CFF.1: 6 residues within 4Å: Chain A: F.3753, E.4239, W.4716, I.4996, W.5011, Y.5014 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.5014 pi-Stacking: A:W.4716, A:W.4716 CFF.6: 6 residues within 4Å: Chain D: F.3753, E.4239, W.4716, I.4996, W.5011, Y.5014 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.5014 pi-Stacking: D:W.4716, D:W.4716 CFF.11: 6 residues within 4Å: Chain G: F.3753, E.4239, W.4716, I.4996, W.5011, Y.5014 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.5014 pi-Stacking: G:W.4716, G:W.4716 CFF.16: 6 residues within 4Å: Chain J: F.3753, E.4239, W.4716, I.4996, W.5011, Y.5014 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Y.5014 pi-Stacking: J:W.4716, J:W.4716

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: E.3893, H.3895, E.3967, Q.3970, T.5001, E.5002, H.5003 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3893, A:E.3967, A:T.5001, A:H.5003 CA.7: 7 residues within 4Å: Chain D: E.3893, H.3895, E.3967, Q.3970, T.5001, E.5002, H.5003 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.3893, D:E.3967, D:T.5001, D:H.5003 CA.12: 7 residues within 4Å: Chain G: E.3893, H.3895, E.3967, Q.3970, T.5001, E.5002, H.5003 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3893, G:E.3967, G:T.5001, G:H.5003 CA.17: 7 residues within 4Å: Chain J: E.3893, H.3895, E.3967, Q.3970, T.5001, E.5002, H.5003 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3893, J:E.3967, J:T.5001, J:H.5003

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

ATP.3: 10 residues within 4Å: Chain A: K.4214, R.4215, M.4954, K.4957, C.4958, F.4959, T.4979, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.4958, A:L.4985 Salt bridges: A:K.4214, A:R.4215 ATP.8: 10 residues within 4Å: Chain D: K.4214, R.4215, M.4954, K.4957, C.4958, F.4959, T.4979, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:C.4958, D:L.4985 Salt bridges: D:K.4214, D:R.4215 ATP.13: 10 residues within 4Å: Chain G: K.4214, R.4215, M.4954, K.4957, C.4958, F.4959, T.4979, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:C.4958, G:L.4985 Salt bridges: G:K.4214, G:R.4215 ATP.18: 10 residues within 4Å: Chain J: K.4214, R.4215, M.4954, K.4957, C.4958, F.4959, T.4979, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:C.4958, J:L.4985 Salt bridges: J:K.4214, J:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4958, A:C.4961, A:H.4978, A:H.4983 ZN.9: 4 residues within 4Å: Chain D: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4958, D:C.4961, D:H.4978, D:H.4983 ZN.14: 4 residues within 4Å: Chain G: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4983 ZN.19: 4 residues within 4Å: Chain J: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4958, J:C.4961, J:H.4978, J:H.4983

4 x F0U: 5-bromanyl-N-[4-chloranyl-2-methyl-6-(methylcarbamoyl)phenyl]-2-(3-chloranylpyridin-2-yl)pyrazole-3-carboxamide(Non-covalent)

F0U.5: 13 residues within 4Å: Chain A: Y.4560, R.4563, F.4564, L.4567, C.4657, Y.4791, L.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.4560, A:L.4567, A:Y.4791, A:L.4792 Hydrogen bonds: A:R.4563, A:Y.4791, A:D.4815, A:D.4815 pi-Cation interactions: A:R.4563 F0U.10: 13 residues within 4Å: Chain D: Y.4560, R.4563, F.4564, L.4567, C.4657, Y.4791, L.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.4560, D:L.4567, D:Y.4791, D:L.4792 Hydrogen bonds: D:R.4563, D:Y.4791, D:D.4815, D:D.4815 pi-Cation interactions: D:R.4563 F0U.15: 13 residues within 4Å: Chain G: Y.4560, R.4563, F.4564, L.4567, C.4657, Y.4791, L.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:Y.4560, G:L.4567, G:Y.4791, G:L.4792 Hydrogen bonds: G:R.4563, G:Y.4791, G:D.4815, G:D.4815 pi-Cation interactions: G:R.4563 F0U.20: 13 residues within 4Å: Chain J: Y.4560, R.4563, F.4564, L.4567, C.4657, Y.4791, L.4792, Y.4795, D.4815, I.4816, M.4818, G.4819, V.4820 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:Y.4560, J:L.4567, J:Y.4791, J:L.4792 Hydrogen bonds: J:R.4563, J:Y.4791, J:D.4815, J:D.4815 pi-Cation interactions: J:R.4563

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, R. et al., Structural basis for diamide modulation of ryanodine receptor. Nat.Chem.Biol. (2020)

Release Date

2020-09-02

Peptides

Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1: ADGJ
Peptidyl-prolyl cis-trans isomerase FKBP1B: BEHK
Calmodulin-1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1,Ryanodine receptor 1

Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

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