SMTL ID : 7tdk.1

Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-inactivated conformation class 3 (Dataset-A)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 7 residues within 4Å: Chain A: R.4215, C.4958, F.4959, I.4960, H.4983, N.4984, L.4985 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.4215, A:N.4984 Salt bridges: A:K.4214, A:R.4215 ACP.5: 8 residues within 4Å: Chain B: R.4215, C.4958, F.4959, I.4960, H.4983, N.4984, L.4985 Ligands: CA.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.4215, B:N.4984 Salt bridges: B:K.4214, B:R.4215 ACP.9: 11 residues within 4Å: Chain C: R.4215, M.4954, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 Ligands: CA.12 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.4215, C:R.4215, C:F.4959, C:N.4984 Salt bridges: C:K.4214 ACP.13: 9 residues within 4Å: Chain D: R.4215, M.4954, C.4958, F.4959, I.4960, H.4983, N.4984, L.4985 Ligands: CA.16 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.4215, D:N.4984 Salt bridges: 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.6: 3 residues within 4Å: Chain B: C.4958, C.4961, H.4978 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4978 ZN.10: 4 residues within 4Å: Chain C: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4983 ZN.14: 5 residues within 4Å: Chain D: C.4958, C.4961, H.4978, E.4982, H.4983 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.4958, D:C.4961, D:H.4983

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 3 residues within 4Å: Chain A: E.3893, E.3967, T.5001 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3893, A:E.3967, A:T.5001 CA.4: 1 residues within 4Å: Chain A: L.4980 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: E.3893, E.3967, T.5001 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.3893, B:E.3967, B:T.5001 CA.8: 1 residues within 4Å: Ligands: ACP.5 No protein-ligand interaction detected (PLIP) CA.11: 3 residues within 4Å: Chain C: E.3893, E.3967, T.5001 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3893, C:E.3967, C:T.5001 CA.12: 1 residues within 4Å: Ligands: ACP.9 No protein-ligand interaction detected (PLIP) CA.15: 3 residues within 4Å: Chain D: E.3893, E.3967, T.5001 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.3893, D:E.3967, D:T.5001 CA.16: 2 residues within 4Å: Chain D: L.4980 Ligands: ACP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, A.R. et al., Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. Elife (2022)

Release Date

2022-03-09

Peptides

Ryanodine receptor 1,Ryanodine receptor 1,RyR1: 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,Ryanodine receptor 1,RyR1

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