SMTL ID : 9e17.1

Structure of RyR1 in the primed state in the presence of caffeine (reprocessed/reanalyzed from EMPIAR-10997, 7TZC, EMD-26205)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.22, A:D.26, A:T.28, A:E.33, A:E.33 CA.2: 6 residues within 4Å: Chain A: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.58, A:D.60, A:T.64, A:E.69, A:E.69 CA.3: 5 residues within 4Å: Chain A: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.95, A:D.97, A:Y.101, A:E.106, A:E.106 CA.4: 6 residues within 4Å: Chain A: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.131, A:D.135, A:Q.137, A:E.142, A:E.142 CA.5: 5 residues within 4Å: Chain C: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.22, C:D.26, C:T.28, C:E.33, C:E.33 CA.6: 6 residues within 4Å: Chain C: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.58, C:D.60, C:T.64, C:E.69, C:E.69 CA.7: 5 residues within 4Å: Chain C: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.95, C:D.97, C:Y.101, C:E.106, C:E.106 CA.8: 6 residues within 4Å: Chain C: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.131, C:D.135, C:Q.137, C:E.142, C:E.142 CA.9: 5 residues within 4Å: Chain D: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.22, D:D.26, D:T.28, D:E.33, D:E.33 CA.10: 6 residues within 4Å: Chain D: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:D.60, D:T.64, D:E.69, D:E.69 CA.11: 5 residues within 4Å: Chain D: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.95, D:D.97, D:Y.101, D:E.106, D:E.106 CA.12: 6 residues within 4Å: Chain D: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.131, D:D.135, D:Q.137, D:E.142, D:E.142 CA.13: 5 residues within 4Å: Chain E: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.22, E:D.26, E:T.28, E:E.33, E:E.33 CA.14: 6 residues within 4Å: Chain E: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.58, E:D.60, E:T.64, E:E.69, E:E.69 CA.15: 5 residues within 4Å: Chain E: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.95, E:D.97, E:Y.101, E:E.106, E:E.106 CA.16: 6 residues within 4Å: Chain E: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.131, E:D.135, E:Q.137, E:E.142, E:E.142 CA.18: 3 residues within 4Å: Chain F: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3893, F:E.3967, F:E.3967, F:T.5001 CA.26: 3 residues within 4Å: Chain J: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3893, J:E.3967, J:E.3967, J:T.5001 CA.34: 3 residues within 4Å: Chain K: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:E.3893, K:E.3967, K:E.3967, K:T.5001 CA.42: 3 residues within 4Å: Chain L: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:E.3893, L:E.3967, L:E.3967, L:T.5001

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

ATP.17: 14 residues within 4Å: Chain F: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:F.4959, F:I.4960, F:T.4979, F:H.4983, F:L.4985 Salt bridges: F:K.4211, F:K.4211, F:K.4214, F:K.4214, F:K.4214, F:R.4215 ATP.21: 11 residues within 4Å: Chain F: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.22 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.886, F:N.921, F:H.993, F:R.1000, F:N.1018, F:N.1035 Salt bridges: F:R.897, F:R.1020 pi-Stacking: F:W.996 ATP.25: 14 residues within 4Å: Chain J: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:F.4959, J:I.4960, J:T.4979, J:H.4983, J:L.4985 Salt bridges: J:K.4211, J:K.4211, J:K.4214, J:K.4214, J:K.4214, J:R.4215 ATP.29: 11 residues within 4Å: Chain J: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.30 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:R.886, J:N.921, J:H.993, J:R.1000, J:N.1018, J:N.1035 Salt bridges: J:R.897, J:R.1020 pi-Stacking: J:W.996 ATP.33: 14 residues within 4Å: Chain K: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:F.4959, K:I.4960, K:T.4979, K:H.4983, K:L.4985 Salt bridges: K:K.4211, K:K.4211, K:K.4214, K:K.4214, K:K.4214, K:R.4215 ATP.37: 11 residues within 4Å: Chain K: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.38 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:R.886, K:N.921, K:H.993, K:R.1000, K:N.1018, K:N.1035 Salt bridges: K:R.897, K:R.1020 pi-Stacking: K:W.996 ATP.41: 14 residues within 4Å: Chain L: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:F.4959, L:I.4960, L:T.4979, L:H.4983, L:L.4985 Salt bridges: L:K.4211, L:K.4211, L:K.4214, L:K.4214, L:K.4214, L:R.4215 ATP.45: 11 residues within 4Å: Chain L: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.46 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:R.886, L:N.921, L:H.993, L:R.1000, L:N.1018, L:N.1035 Salt bridges: L:R.897, L:R.1020 pi-Stacking: L:W.996

4 x ZN: ZINC ION(Non-covalent)

ZN.19: 4 residues within 4Å: Chain F: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4958, F:C.4961, F:H.4978, F:H.4983 ZN.27: 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 ZN.35: 4 residues within 4Å: Chain K: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4958, K:C.4961, K:H.4978, K:H.4983 ZN.43: 4 residues within 4Å: Chain L: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.4958, L:C.4961, L:H.4978, L:H.4983

4 x CFF: CAFFEINE(Non-covalent)

CFF.20: 5 residues within 4Å: Chain F: F.3753, E.4239, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain F pi-Stacking: F:W.4716, F:W.4716, F:W.4716 CFF.28: 5 residues within 4Å: Chain J: F.3753, E.4239, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain J pi-Stacking: J:W.4716, J:W.4716, J:W.4716 CFF.36: 5 residues within 4Å: Chain K: F.3753, E.4239, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain K pi-Stacking: K:W.4716, K:W.4716, K:W.4716 CFF.44: 5 residues within 4Å: Chain L: F.3753, E.4239, W.4716, I.4996, W.5011 3 PLIP interactions: 3 interactions with chain L pi-Stacking: L:W.4716, L:W.4716, L:W.4716

4 x KVR: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid(Non-covalent)

KVR.22: 10 residues within 4Å: Chain F: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.21 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:W.882, F:Y.920 Hydrogen bonds: F:E.917 Salt bridges: F:H.879, F:H.904 pi-Cation interactions: F:W.882 KVR.30: 10 residues within 4Å: Chain J: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.29 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:W.882, J:Y.920 Hydrogen bonds: J:E.917 Salt bridges: J:H.879, J:H.904 pi-Cation interactions: J:W.882 KVR.38: 10 residues within 4Å: Chain K: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.37 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:W.882, K:Y.920 Hydrogen bonds: K:E.917 Salt bridges: K:H.879, K:H.904 pi-Cation interactions: K:W.882 KVR.46: 10 residues within 4Å: Chain L: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.45 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:W.882, L:Y.920 Hydrogen bonds: L:E.917 Salt bridges: L:H.879, L:H.904 pi-Cation interactions: L:W.882

8 x L9R: (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

L9R.23: 13 residues within 4Å: Chain F: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Chain K: Y.4630, N.4805 Ligands: L9R.40 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.4847, F:L.4850, F:Y.4851, F:Y.4851, F:F.4858, F:F.4858, F:F.4859, F:Y.4912, F:F.4916, F:F.4923 Hydrogen bonds: F:Y.4909 L9R.24: 14 residues within 4Å: Chain F: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Chain J: L.4850, V.4853, N.4857, F.4858 Ligands: L9R.31 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain J Hydrophobic interactions: F:V.4797, F:L.4801, F:L.4801, F:F.4808, F:A.4811, F:L.4814, J:L.4850, J:V.4853, J:F.4858 Hydrogen bonds: F:N.4805 L9R.31: 13 residues within 4Å: Chain F: Y.4630, N.4805 Chain J: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Ligands: L9R.24 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:V.4847, J:L.4850, J:Y.4851, J:Y.4851, J:F.4858, J:F.4858, J:F.4859, J:Y.4912, J:F.4916, J:F.4923 Hydrogen bonds: J:Y.4909 L9R.32: 13 residues within 4Å: Chain J: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Chain L: V.4853, N.4857, F.4858 Ligands: L9R.47 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain L Hydrophobic interactions: J:V.4797, J:L.4801, J:L.4801, J:F.4808, J:A.4811, J:L.4814, L:V.4853, L:F.4858 Hydrogen bonds: J:N.4805 L9R.39: 13 residues within 4Å: Chain K: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Chain L: Y.4630, N.4805 Ligands: L9R.48 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:V.4847, K:L.4850, K:Y.4851, K:Y.4851, K:F.4858, K:F.4858, K:F.4859, K:Y.4912, K:F.4916, K:F.4923 Hydrogen bonds: K:Y.4909 L9R.40: 12 residues within 4Å: Chain F: N.4857, F.4858 Chain K: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Ligands: L9R.23 8 PLIP interactions: 7 interactions with chain K, 1 interactions with chain F Hydrophobic interactions: K:V.4797, K:L.4801, K:L.4801, K:F.4808, K:A.4811, K:L.4814, F:F.4858 Hydrogen bonds: K:N.4805 L9R.47: 13 residues within 4Å: Chain J: Y.4630, N.4805 Chain L: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Ligands: L9R.32 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:V.4847, L:L.4850, L:Y.4851, L:Y.4851, L:F.4858, L:F.4858, L:F.4859, L:Y.4912, L:F.4916, L:F.4923 Hydrogen bonds: L:Y.4909 L9R.48: 14 residues within 4Å: Chain K: L.4850, V.4853, N.4857, F.4858 Chain L: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Ligands: L9R.39 10 PLIP interactions: 3 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:L.4850, K:V.4853, K:F.4858, L:V.4797, L:L.4801, L:L.4801, L:F.4808, L:A.4811, L:L.4814 Hydrogen bonds: L:N.4805

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Targeting ryanodine receptors with allopurinol and xanthine derivatives for the treatment of cardiac and musculoskeletal weakness disorders. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2024-10-30

Peptides

Calmodulin-1: ACDE
Peptidyl-prolyl cis-trans isomerase FKBP1A: BGHI
Ryanodine receptor 1: FJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
D

D
E

E
C

B
F

G
H

H
J

I
O

F
A

J
B

K
G

L
I

Membrane

We predict this structure to be a membrane protein.
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Calmodulin-1

Peptidyl-prolyl cis-trans isomerase FKBP1A

Ryanodine receptor 1

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