SMTL ID : 8uq3.1

Structure of human RyR2-S2808D in the closed state in the presence of ARM210

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 A: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4888, A:C.4891, A:H.4908, A:H.4913 ZN.5: 4 residues within 4Å: Chain F: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4888, F:C.4891, F:H.4908, F:H.4913 ZN.9: 4 residues within 4Å: Chain G: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4888, G:C.4891, G:H.4908, G:H.4913 ZN.13: 4 residues within 4Å: Chain H: C.4888, C.4891, H.4908, H.4913 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4888, H:C.4891, H:H.4908, H:H.4913

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

ATP.2: 12 residues within 4Å: Chain A: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.4170, A:F.4889, A:I.4890, A:H.4913, A:L.4915 Salt bridges: A:K.4166, A:K.4169, A:K.4169, A:K.4169 ATP.3: 7 residues within 4Å: Chain A: W.893, E.928, Y.931, M.935, R.1011, W.1016 Ligands: KVR.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.932 Salt bridges: A:R.1011, A:R.1011 pi-Stacking: A:W.893, A:W.893 ATP.6: 12 residues within 4Å: Chain F: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.4170, F:F.4889, F:I.4890, F:H.4913, F:L.4915 Salt bridges: F:K.4166, F:K.4169, F:K.4169, F:K.4169 ATP.7: 7 residues within 4Å: Chain F: W.893, E.928, Y.931, M.935, R.1011, W.1016 Ligands: KVR.8 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.932 Salt bridges: F:R.1011, F:R.1011 pi-Stacking: F:W.893, F:W.893 ATP.10: 12 residues within 4Å: Chain G: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:R.4170, G:F.4889, G:I.4890, G:H.4913, G:L.4915 Salt bridges: G:K.4166, G:K.4169, G:K.4169, G:K.4169 ATP.11: 7 residues within 4Å: Chain G: W.893, E.928, Y.931, M.935, R.1011, W.1016 Ligands: KVR.12 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:N.932 Salt bridges: G:R.1011, G:R.1011 pi-Stacking: G:W.893, G:W.893 ATP.14: 12 residues within 4Å: Chain H: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:R.4170, H:F.4889, H:I.4890, H:H.4913, H:L.4915 Salt bridges: H:K.4166, H:K.4169, H:K.4169, H:K.4169 ATP.15: 7 residues within 4Å: Chain H: W.893, E.928, Y.931, M.935, R.1011, W.1016 Ligands: KVR.16 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:N.932 Salt bridges: H:R.1011, H:R.1011 pi-Stacking: H:W.893, H:W.893

4 x KVR: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid(Non-covalent)

KVR.4: 5 residues within 4Å: Chain A: W.893, H.915, W.1007, R.1031 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.1007 Salt bridges: A:R.1031 pi-Stacking: A:W.893 KVR.8: 5 residues within 4Å: Chain F: W.893, H.915, W.1007, R.1031 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.1007 Salt bridges: F:R.1031 pi-Stacking: F:W.893 KVR.12: 5 residues within 4Å: Chain G: W.893, H.915, W.1007, R.1031 Ligands: ATP.11 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:W.1007 Salt bridges: G:R.1031 pi-Stacking: G:W.893 KVR.16: 5 residues within 4Å: Chain H: W.893, H.915, W.1007, R.1031 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:W.1007 Salt bridges: H:R.1031 pi-Stacking: H:W.893

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders. Nat Commun (2024)

Release Date

2023-11-15

Peptides

Ryanodine receptor 2: AFGH
Peptidyl-prolyl cis-trans isomerase FKBP1B: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
C

H
D

B
E

C
F

D
G

E
H

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 2

Peptidyl-prolyl cis-trans isomerase FKBP1B

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