SMTL ID : 9nmp.1

Structure of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain E: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4956, E:C.4959, E:H.4976, E:H.4981 ZN.10: 4 residues within 4Å: Chain F: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4956, F:C.4959, F:H.4976, F:H.4981 ZN.19: 4 residues within 4Å: Chain G: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4956, G:C.4959, G:H.4976, G:H.4981 ZN.28: 4 residues within 4Å: Chain H: C.4956, C.4959, H.4976, H.4981 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4956, H:C.4959, H:H.4976, H:H.4981

4 x CFF: CAFFEINE(Non-covalent)

CFF.2: 6 residues within 4Å: Chain E: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 4 PLIP interactions: 4 interactions with chain E pi-Stacking: E:W.4714, E:W.4714, E:W.4714, E:W.4714 CFF.11: 6 residues within 4Å: Chain F: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 4 PLIP interactions: 4 interactions with chain F pi-Stacking: F:W.4714, F:W.4714, F:W.4714, F:W.4714 CFF.20: 6 residues within 4Å: Chain G: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 4 PLIP interactions: 4 interactions with chain G pi-Stacking: G:W.4714, G:W.4714, G:W.4714, G:W.4714 CFF.29: 6 residues within 4Å: Chain H: F.3756, E.4242, I.4245, W.4714, I.4994, W.5009 4 PLIP interactions: 4 interactions with chain H pi-Stacking: H:W.4714, H:W.4714, H:W.4714, H:W.4714

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

ATP.3: 14 residues within 4Å: Chain E: K.4214, K.4217, R.4218, M.4952, E.4953, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:E.4953, E:F.4957, E:I.4958, E:T.4977, E:T.4977, E:H.4981, E:L.4983 Salt bridges: E:K.4214, E:K.4214, E:K.4217, E:K.4217, E:K.4217, E:R.4218 ATP.7: 8 residues within 4Å: Chain E: W.883, R.887, R.898, H.905, C.907, Y.921, W.997, R.1021 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:W.883, E:Y.921, E:W.997, E:R.1021 Salt bridges: E:R.887, E:R.898, E:H.905, E:H.905, E:R.1021 ATP.12: 14 residues within 4Å: Chain F: K.4214, K.4217, R.4218, M.4952, E.4953, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:E.4953, F:F.4957, F:I.4958, F:T.4977, F:T.4977, F:H.4981, F:L.4983 Salt bridges: F:K.4214, F:K.4214, F:K.4217, F:K.4217, F:K.4217, F:R.4218 ATP.16: 8 residues within 4Å: Chain F: W.883, R.887, R.898, H.905, C.907, Y.921, W.997, R.1021 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:W.883, F:Y.921, F:W.997, F:R.1021 Salt bridges: F:R.887, F:R.898, F:H.905, F:H.905, F:R.1021 ATP.21: 14 residues within 4Å: Chain G: K.4214, K.4217, R.4218, M.4952, E.4953, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:E.4953, G:F.4957, G:I.4958, G:T.4977, G:T.4977, G:H.4981, G:L.4983 Salt bridges: G:K.4214, G:K.4214, G:K.4217, G:K.4217, G:K.4217, G:R.4218 ATP.25: 8 residues within 4Å: Chain G: W.883, R.887, R.898, H.905, C.907, Y.921, W.997, R.1021 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:W.883, G:Y.921, G:W.997, G:R.1021 Salt bridges: G:R.887, G:R.898, G:H.905, G:H.905, G:R.1021 ATP.30: 14 residues within 4Å: Chain H: K.4214, K.4217, R.4218, M.4952, E.4953, K.4955, C.4956, F.4957, I.4958, F.4973, T.4977, H.4981, N.4982, L.4983 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:E.4953, H:F.4957, H:I.4958, H:T.4977, H:T.4977, H:H.4981, H:L.4983 Salt bridges: H:K.4214, H:K.4214, H:K.4217, H:K.4217, H:K.4217, H:R.4218 ATP.34: 8 residues within 4Å: Chain H: W.883, R.887, R.898, H.905, C.907, Y.921, W.997, R.1021 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:W.883, H:Y.921, H:W.997, H:R.1021 Salt bridges: H:R.887, H:R.898, H:H.905, H:H.905, H:R.1021

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain E: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.3896, E:E.3896, E:E.3970, E:T.4999 CA.13: 3 residues within 4Å: Chain F: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3896, F:E.3896, F:E.3970, F:T.4999 CA.22: 3 residues within 4Å: Chain G: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3896, G:E.3896, G:E.3970, G:T.4999 CA.31: 3 residues within 4Å: Chain H: E.3896, E.3970, T.4999 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.3896, H:E.3896, H:E.3970, H:T.4999

8 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.5: 15 residues within 4Å: Chain E: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Chain H: Y.4628 Ligands: PCW.33 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:V.4845, E:L.4848, E:Y.4849, E:Y.4849, E:F.4856, E:F.4856, E:Y.4910, E:Y.4910, E:Y.4910, E:V.4913, E:F.4914, E:F.4921 Hydrogen bonds: E:Y.4907 PCW.6: 12 residues within 4Å: Chain E: M.4796, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain F: L.4848, V.4851, N.4855, F.4856 Ligands: 01.8, PCW.14 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:L.4848, F:L.4848, F:V.4851, F:N.4855, F:F.4856, F:F.4856, E:F.4805, E:F.4806, E:F.4806, E:L.4812 Hydrogen bonds: E:N.4803 PCW.14: 15 residues within 4Å: Chain E: Y.4628 Chain F: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Ligands: PCW.6 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:V.4845, F:L.4848, F:Y.4849, F:Y.4849, F:F.4856, F:F.4856, F:Y.4910, F:Y.4910, F:Y.4910, F:V.4913, F:F.4914, F:F.4921 Hydrogen bonds: F:Y.4907 PCW.15: 12 residues within 4Å: Chain F: M.4796, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain G: L.4848, V.4851, N.4855, F.4856 Ligands: 01.17, PCW.23 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: F:F.4805, F:F.4806, F:F.4806, F:L.4812, G:V.4851, G:N.4855, G:F.4856, G:F.4856 Hydrogen bonds: F:N.4803 PCW.23: 15 residues within 4Å: Chain F: Y.4628 Chain G: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Ligands: PCW.15 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:V.4845, G:L.4848, G:Y.4849, G:Y.4849, G:F.4856, G:F.4856, G:Y.4910, G:Y.4910, G:Y.4910, G:V.4913, G:F.4914, G:F.4921 Hydrogen bonds: G:Y.4907 PCW.24: 12 residues within 4Å: Chain G: M.4796, Y.4802, N.4803, F.4805, F.4806, L.4812 Chain H: L.4848, V.4851, N.4855, F.4856 Ligands: 01.26, PCW.32 11 PLIP interactions: 6 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:L.4848, H:L.4848, H:V.4851, H:N.4855, H:F.4856, H:F.4856, G:F.4805, G:F.4806, G:F.4806, G:L.4812 Hydrogen bonds: G:N.4803 PCW.32: 15 residues within 4Å: Chain G: Y.4628 Chain H: V.4845, L.4848, Y.4849, V.4852, N.4855, F.4856, F.4857, Y.4907, Y.4910, V.4913, F.4914, T.4917, F.4921 Ligands: PCW.24 13 PLIP interactions: 13 interactions with chain H Hydrophobic interactions: H:V.4845, H:L.4848, H:Y.4849, H:Y.4849, H:F.4856, H:F.4856, H:Y.4910, H:Y.4910, H:Y.4910, H:V.4913, H:F.4914, H:F.4921 Hydrogen bonds: H:Y.4907 PCW.33: 12 residues within 4Å: Chain E: L.4848, V.4851, N.4855, F.4856 Chain H: M.4796, Y.4802, N.4803, F.4805, F.4806, L.4812 Ligands: PCW.5, 01.35 11 PLIP interactions: 5 interactions with chain H, 6 interactions with chain E Hydrophobic interactions: H:F.4805, H:F.4806, H:F.4806, H:L.4812, E:L.4848, E:L.4848, E:V.4851, E:N.4855, E:F.4856, E:F.4856 Hydrogen bonds: H:N.4803

8 x 01: (1S,3R,7S,8S,8aR)-8-{2-[(2R,4R)-4-hydroxy-6-oxooxan-2-yl]ethyl}-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl 2,2-dimethylbutanoate

01.8: 9 residues within 4Å: Chain E: N.4785, L.4788, Y.4789, W.4792, Y.4793, M.4796, A.4809, L.4812 Ligands: PCW.6 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.4792, E:Y.4793, E:L.4812 Hydrogen bonds: E:W.4792 01.9: 3 residues within 4Å: Chain E: L.4909, Y.4910, V.4913 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.4910, E:Y.4910, E:V.4913 Hydrogen bonds: E:Y.4910 01.17: 9 residues within 4Å: Chain F: N.4785, L.4788, Y.4789, W.4792, Y.4793, M.4796, A.4809, L.4812 Ligands: PCW.15 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:W.4792, F:Y.4793, F:L.4812 Hydrogen bonds: F:W.4792 01.18: 3 residues within 4Å: Chain F: L.4909, Y.4910, V.4913 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.4910, F:Y.4910, F:V.4913 Hydrogen bonds: F:Y.4910 01.26: 9 residues within 4Å: Chain G: N.4785, L.4788, Y.4789, W.4792, Y.4793, M.4796, A.4809, L.4812 Ligands: PCW.24 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:W.4792, G:Y.4793, G:L.4812 Hydrogen bonds: G:W.4792 01.27: 3 residues within 4Å: Chain G: L.4909, Y.4910, V.4913 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.4910, G:Y.4910, G:V.4913 Hydrogen bonds: G:Y.4910 01.35: 9 residues within 4Å: Chain H: N.4785, L.4788, Y.4789, W.4792, Y.4793, M.4796, A.4809, L.4812 Ligands: PCW.33 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:W.4792, H:Y.4793, H:L.4812 Hydrogen bonds: H:W.4792 01.36: 3 residues within 4Å: Chain H: L.4909, Y.4910, V.4913 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:Y.4910, H:Y.4910, H:V.4913 Hydrogen bonds: H:Y.4910

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weninger, G., Structural basis for statin-induced skeletal muscle weakness. To Be Published

Release Date

2025-10-08

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1A: ABCD
Ryanodine receptor 1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
D

F
A

G
B

H
C

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1A

Ryanodine receptor 1

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