SMTL ID : 7u9z.1

Structure of PKA phosphorylated human RyR2-R2474S in the open state

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.6: 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.11: 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.16: 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)(Covalent)

ATP.2: 12 residues within 4Å: Chain A: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.4885, A:E.4885, A:F.4889, A:T.4909, A:L.4915 Salt bridges: A:K.4169, A:K.4169, A:R.4170 ATP.5: 8 residues within 4Å: Chain A: H.915, E.928, Y.931, N.932, W.1007, R.1011, N.1029, R.1031 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.928, A:W.1007, A:N.1029 Salt bridges: A:R.1011, A:R.1031, A:R.1031 ATP.7: 12 residues within 4Å: Chain F: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.4885, F:E.4885, F:F.4889, F:T.4909, F:L.4915 Salt bridges: F:K.4169, F:K.4169, F:R.4170 ATP.10: 9 residues within 4Å: Chain F: H.915, C.917, E.928, Y.931, N.932, W.1007, R.1011, N.1029, R.1031 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:E.928, F:W.1007, F:N.1029 Salt bridges: F:R.1011, F:R.1031, F:R.1031 ATP.12: 12 residues within 4Å: Chain G: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:E.4885, G:E.4885, G:F.4889, G:T.4909, G:L.4915 Salt bridges: G:K.4169, G:K.4169, G:R.4170 ATP.15: 8 residues within 4Å: Chain G: H.915, E.928, Y.931, N.932, W.1007, R.1011, N.1029, R.1031 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:E.928, G:W.1007, G:N.1029 Salt bridges: G:R.1011, G:R.1031, G:R.1031 ATP.17: 12 residues within 4Å: Chain H: K.4169, R.4170, M.4884, E.4885, K.4887, C.4888, F.4889, F.4905, T.4909, H.4913, N.4914, L.4915 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:E.4885, H:E.4885, H:F.4889, H:T.4909, H:L.4915 Salt bridges: H:K.4169, H:K.4169, H:R.4170 ATP.20: 9 residues within 4Å: Chain H: H.915, C.917, E.928, Y.931, N.932, W.1007, R.1011, N.1029, R.1031 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:E.928, H:W.1007, H:N.1029 Salt bridges: H:R.1011, H:R.1031, H:R.1031

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.3848, A:E.3922, A:T.4931 CA.8: 4 residues within 4Å: Chain F: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3848, F:E.3922, F:T.4931 CA.13: 4 residues within 4Å: Chain G: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3848, G:E.3922, G:T.4931 CA.18: 4 residues within 4Å: Chain H: E.3848, E.3922, Q.3925, T.4931 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3848, H:E.3922, H:T.4931

4 x XAN: XANTHINE(Non-covalent)

XAN.4: 5 residues within 4Å: Chain A: E.4194, Q.4201, W.4645, I.4926, Y.4944 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.4201, A:Y.4944, A:Y.4944, A:Y.4944 pi-Stacking: A:W.4645, A:W.4645, A:W.4645 XAN.9: 5 residues within 4Å: Chain F: E.4194, Q.4201, W.4645, I.4926, Y.4944 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:Q.4201, F:Y.4944, F:Y.4944, F:Y.4944 pi-Stacking: F:W.4645, F:W.4645, F:W.4645 XAN.14: 5 residues within 4Å: Chain G: E.4194, Q.4201, W.4645, I.4926, Y.4944 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:Q.4201, G:Y.4944, G:Y.4944, G:Y.4944 pi-Stacking: G:W.4645, G:W.4645, G:W.4645 XAN.19: 5 residues within 4Å: Chain H: E.4194, Q.4201, W.4645, I.4926, Y.4944 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:Q.4201, H:Y.4944, H:Y.4944, H:Y.4944 pi-Stacking: H:W.4645, H:W.4645, H:W.4645

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miotto, M.C. et al., Structural analyses of human ryanodine receptor type 2 channels reveal the mechanisms for sudden cardiac death and treatment. Sci Adv (2022)

Release Date

2022-08-03

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

Ryanodine receptor 2

Peptidyl-prolyl cis-trans isomerase FKBP1B

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