SMTL ID : 8sew.1

Cryo-EM Structure of RyR1 + ADP (Local Refinement of TMD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.4959, A:I.4960, A:T.4979, A:H.4983, A:L.4985 Salt bridges: A:K.4214, A:K.4214, A:R.4215 ADP.3: 12 residues within 4Å: Chain B: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.4959, B:I.4960, B:T.4979, B:H.4983, B:L.4985 Salt bridges: B:K.4214, B:K.4214, B:R.4215 ADP.5: 12 residues within 4Å: Chain C: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:F.4959, C:I.4960, C:T.4979, C:H.4983, C:L.4985 Salt bridges: C:K.4214, C:K.4214, C:R.4215 ADP.7: 12 residues within 4Å: Chain D: K.4211, K.4214, M.4954, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:F.4959, D:I.4960, D:T.4979, D:H.4983, D:L.4985 Salt bridges: D:K.4214, D:K.4214, D:R.4215

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.4: 4 residues within 4Å: Chain B: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4978, B:H.4983 ZN.6: 4 residues within 4Å: Chain C: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4978, C:H.4983 ZN.8: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cholak, S. et al., Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives. Structure (2023)

Release Date

2023-05-24

Peptides

Ryanodine receptor 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

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

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