SMTL ID : 7tdh.1

Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.4961, H.4978, E.4982, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4961, A:H.4978, A:H.4983, A:C.5027 ZN.5: 5 residues within 4Å: Chain B: C.4958, C.4961, H.4978, H.4983, C.5027 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4978 ZN.9: 5 residues within 4Å: Chain C: C.4961, H.4978, E.4982, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.4961, C:H.4978, C:H.4983, C:C.5027 ZN.13: 5 residues within 4Å: Chain D: C.4961, H.4978, E.4982, H.4983, C.5027 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4961, D:H.4978, D:H.4983, D:C.5027

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

CA.2: 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.3: 1 residues within 4Å: Ligands: ACP.4 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain B: Q.3889, E.3893, E.3967, T.5001 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.3893, B:T.5001 CA.7: 1 residues within 4Å: Ligands: ACP.8 No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain C: E.3893, E.3967, Q.3970, T.5001, H.5003 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.3893, C:E.3893, C:T.5001 CA.11: 1 residues within 4Å: Ligands: ACP.12 No protein-ligand interaction detected (PLIP) CA.14: 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.15: 1 residues within 4Å: Ligands: ACP.16 No protein-ligand interaction detected (PLIP)

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

ACP.4: 9 residues within 4Å: Chain A: K.4214, R.4215, M.4954, C.4958, T.4979, H.4983, N.4984, L.4985 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.4215, A:R.4215, A:T.4979, A:N.4984 Salt bridges: A:K.4214 ACP.8: 8 residues within 4Å: Chain B: K.4214, R.4215, M.4954, C.4958, T.4979, N.4984, L.4985 Ligands: CA.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.4214, B:R.4215, B:R.4215, B:C.4958, B:T.4979 Salt bridges: B:K.4214 ACP.12: 6 residues within 4Å: Chain C: M.4954, C.4958, T.4979, N.4984, L.4985 Ligands: CA.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.4958, C:T.4979 Salt bridges: C:K.4214 ACP.16: 5 residues within 4Å: Chain D: M.4954, C.4958, T.4979, L.4985 Ligands: CA.15 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:C.4958, D:T.4979

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.
Show / Hide

Ryanodine receptor 1,Ryanodine receptor 1,RyR1

Related Entries With Identical Sequence