SMTL ID : 9e19.1

Structure of RyR1 in the open state in the presence of pentoxifylline

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.4959, A:H.4983, A:L.4985 Salt bridges: A:K.4211, A:K.4211, A:K.4214, A:K.4214, A:K.4214, A:R.4215 ATP.5: 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 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:F.4959, 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.9: 14 residues within 4Å: Chain G: 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 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:F.4959, G:H.4983, G:L.4985 Salt bridges: G:K.4211, G:K.4211, G:K.4214, G:K.4214, G:K.4214, G:R.4215 ATP.13: 14 residues within 4Å: Chain H: 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 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:F.4959, H:H.4983, H:L.4985 Salt bridges: H:K.4211, H:K.4211, H:K.4214, H:K.4214, H:K.4214, H:R.4215

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.3893, H.3895, E.3967, T.5001, H.5003 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3893, A:E.3967, A:T.5001 CA.6: 5 residues within 4Å: Chain F: E.3893, H.3895, E.3967, T.5001, H.5003 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3893, F:E.3967, F:T.5001 CA.10: 5 residues within 4Å: Chain G: E.3893, H.3895, E.3967, T.5001, H.5003 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3893, G:E.3967, G:T.5001 CA.14: 5 residues within 4Å: Chain H: E.3893, H.3895, E.3967, T.5001, H.5003 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3893, H:E.3967, H:T.5001

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.4958, C.4961, F.4968, H.4978 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4958, A:C.4961, A:H.4978, A:H.4978 ZN.7: 4 residues within 4Å: Chain F: C.4958, C.4961, F.4968, H.4978 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4958, F:C.4961, F:H.4978, F:H.4978 ZN.11: 4 residues within 4Å: Chain G: C.4958, C.4961, F.4968, H.4978 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4978 ZN.15: 4 residues within 4Å: Chain H: C.4958, C.4961, F.4968, H.4978 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4958, H:C.4961, H:H.4978, H:H.4978

4 x PNX: 3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE(Non-covalent)

PNX.4: 10 residues within 4Å: Chain A: F.3753, V.4235, E.4239, R.4679, W.4716, I.4996, W.5011, Y.5014, R.5017, W.5019 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.4235, A:W.4716, A:W.5019 pi-Stacking: A:W.4716, A:W.4716, A:W.4716 PNX.8: 10 residues within 4Å: Chain F: F.3753, V.4235, E.4239, R.4679, W.4716, I.4996, W.5011, Y.5014, R.5017, W.5019 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.4235, F:W.4716, F:W.5019 pi-Stacking: F:W.4716, F:W.4716, F:W.4716 PNX.12: 10 residues within 4Å: Chain G: F.3753, V.4235, E.4239, R.4679, W.4716, I.4996, W.5011, Y.5014, R.5017, W.5019 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.4235, G:W.4716, G:W.5019 pi-Stacking: G:W.4716, G:W.4716, G:W.4716 PNX.16: 10 residues within 4Å: Chain H: F.3753, V.4235, E.4239, R.4679, W.4716, I.4996, W.5011, Y.5014, R.5017, W.5019 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:V.4235, H:W.4716, H:W.5019 pi-Stacking: H:W.4716, H:W.4716, H:W.4716

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C., Targeting Ryanodine Receptors with Allopurinol and Xanthine Derivatives for the Treatment of Cardiac and Musculoskeletal Weakness Disorders. To Be Published

Release Date

2024-10-30

Peptides

Ryanodine receptor 1: AFGH
Peptidyl-prolyl cis-trans isomerase FKBP1A: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
D

H
C

B
E

C
H

D
G

E
F

Membrane

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

Peptidyl-prolyl cis-trans isomerase FKBP1A

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