SMTL ID : 8uxg.1

Structure of PKA phosphorylated human RyR2-R420W 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: 14 residues within 4Å: Chain A: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, F.4905, E.4906, T.4909, H.4913, N.4914, L.4915 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.4889, A:I.4890, A:E.4906, A:T.4909, A:H.4913, A:L.4915 Salt bridges: A:K.4166, A:K.4166, A:K.4169, A:K.4169, A:R.4170 ATP.3: 11 residues within 4Å: Chain A: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029, R.1031 Ligands: KVR.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.928, A:Y.931, A:W.1007, A:R.1011, A:Q.1014, A:W.1016, A:N.1029, A:R.1031 Salt bridges: A:R.1011, A:R.1011, A:R.1011 pi-Stacking: A:Y.931 ATP.6: 14 residues within 4Å: Chain F: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, F.4905, E.4906, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:F.4889, F:E.4906, F:T.4909, F:H.4913, F:L.4915 Salt bridges: F:K.4166, F:K.4166, F:K.4169, F:K.4169, F:R.4170 ATP.7: 11 residues within 4Å: Chain F: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029, R.1031 Ligands: KVR.8 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:E.928, F:Y.931, F:W.1007, F:R.1011, F:Q.1014, F:W.1016, F:N.1029, F:R.1031 Salt bridges: F:R.1011, F:R.1011, F:R.1011 pi-Stacking: F:Y.931 ATP.10: 14 residues within 4Å: Chain G: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, F.4905, E.4906, T.4909, H.4913, N.4914, L.4915 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:F.4889, G:E.4906, G:T.4909, G:H.4913, G:L.4915 Salt bridges: G:K.4166, G:K.4166, G:K.4169, G:K.4169, G:R.4170 ATP.11: 11 residues within 4Å: Chain G: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029, R.1031 Ligands: KVR.12 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:E.928, G:Y.931, G:W.1007, G:R.1011, G:Q.1014, G:W.1016, G:N.1029, G:R.1031 Salt bridges: G:R.1011, G:R.1011, G:R.1011 pi-Stacking: G:Y.931 ATP.14: 14 residues within 4Å: Chain H: K.4166, K.4169, R.4170, M.4884, K.4887, C.4888, F.4889, I.4890, F.4905, E.4906, T.4909, H.4913, N.4914, L.4915 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:F.4889, H:I.4890, H:E.4906, H:T.4909, H:H.4913, H:L.4915 Salt bridges: H:K.4166, H:K.4166, H:K.4169, H:K.4169, H:R.4170 ATP.15: 11 residues within 4Å: Chain H: E.928, Y.931, N.932, M.935, W.1007, R.1011, Q.1014, W.1016, N.1029, R.1031 Ligands: KVR.16 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:E.928, H:Y.931, H:W.1007, H:R.1011, H:Q.1014, H:W.1016, H:N.1029, H:R.1031 Salt bridges: H:R.1011, H:R.1011, H:R.1011 pi-Stacking: H:Y.931

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

KVR.4: 7 residues within 4Å: Chain A: H.890, W.893, K.897, C.917, N.932, M.935 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.932 pi-Stacking: A:W.893, A:W.893 KVR.8: 7 residues within 4Å: Chain F: H.890, W.893, K.897, C.917, N.932, M.935 Ligands: ATP.7 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:N.932 pi-Stacking: F:W.893, F:W.893 KVR.12: 7 residues within 4Å: Chain G: H.890, W.893, K.897, C.917, N.932, M.935 Ligands: ATP.11 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:N.932 pi-Stacking: G:W.893, G:W.893 KVR.16: 7 residues within 4Å: Chain H: H.890, W.893, K.897, C.917, N.932, M.935 Ligands: ATP.15 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:N.932 pi-Stacking: H:W.893, 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

2023-11-22

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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