SMTL ID : 6jiu.1

Structure of RyR2 (F/A/C/L-Ca2+/Ca2+CaM dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.4889, I.4891, C.4892, G.4893, H.4914 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.4889, A:C.4892, A:H.4914, A:H.4914 ZN.7: 5 residues within 4Å: Chain D: C.4889, I.4891, C.4892, G.4893, H.4914 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.4889, D:C.4892, D:H.4914, D:H.4914 ZN.13: 5 residues within 4Å: Chain G: C.4889, I.4891, C.4892, G.4893, H.4914 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4889, G:C.4892, G:H.4914, G:H.4914 ZN.19: 5 residues within 4Å: Chain J: C.4889, I.4891, C.4892, G.4893, H.4914 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.4889, J:C.4892, J:H.4914, J:H.4914

12 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3849, A:E.3923, A:E.3923, A:T.4932 CA.5: 5 residues within 4Å: Chain C: D.23, T.27, I.28, T.29, E.32 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.27, C:E.32 CA.6: 3 residues within 4Å: Chain C: T.27, N.61, D.65 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain D: E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.3849, D:E.3923, D:E.3923, D:T.4932 CA.11: 5 residues within 4Å: Chain F: D.23, T.27, I.28, T.29, E.32 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.27, F:E.32 CA.12: 3 residues within 4Å: Chain F: T.27, N.61, D.65 No protein-ligand interaction detected (PLIP) CA.14: 3 residues within 4Å: Chain G: E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3849, G:E.3923, G:E.3923, G:T.4932 CA.17: 5 residues within 4Å: Chain I: D.23, T.27, I.28, T.29, E.32 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.27, I:E.32 CA.18: 3 residues within 4Å: Chain I: T.27, N.61, D.65 No protein-ligand interaction detected (PLIP) CA.20: 3 residues within 4Å: Chain J: E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3849, J:E.3923, J:E.3923, J:T.4932 CA.23: 5 residues within 4Å: Chain L: D.23, T.27, I.28, T.29, E.32 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:T.27, L:E.32 CA.24: 3 residues within 4Å: Chain L: T.27, N.61, D.65 No protein-ligand interaction detected (PLIP)

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

ATP.3: 9 residues within 4Å: Chain A: K.4167, K.4170, R.4171, I.4174, M.4885, C.4889, F.4890, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.4890, A:T.4910 Salt bridges: A:K.4167, A:K.4170, A:K.4170, A:R.4171, A:R.4171 ATP.9: 9 residues within 4Å: Chain D: K.4167, K.4170, R.4171, I.4174, M.4885, C.4889, F.4890, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:F.4890, D:T.4910 Salt bridges: D:K.4167, D:K.4170, D:K.4170, D:R.4171, D:R.4171 ATP.15: 9 residues within 4Å: Chain G: K.4167, K.4170, R.4171, I.4174, M.4885, C.4889, F.4890, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:F.4890, G:T.4910 Salt bridges: G:K.4167, G:K.4170, G:K.4170, G:R.4171, G:R.4171 ATP.21: 9 residues within 4Å: Chain J: K.4167, K.4170, R.4171, I.4174, M.4885, C.4889, F.4890, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:F.4890, J:T.4910 Salt bridges: J:K.4167, J:K.4170, J:K.4170, J:R.4171, J:R.4171

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain A: F.3715, E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.4195 pi-Stacking: A:W.4646, A:W.4646, A:W.4646 CFF.10: 6 residues within 4Å: Chain D: F.3715, E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.4195 pi-Stacking: D:W.4646, D:W.4646, D:W.4646 CFF.16: 6 residues within 4Å: Chain G: F.3715, E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:E.4195 pi-Stacking: G:W.4646, G:W.4646, G:W.4646 CFF.22: 6 residues within 4Å: Chain J: F.3715, E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:E.4195 pi-Stacking: J:W.4646, J:W.4646, J:W.4646

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, D. et al., Modulation of cardiac ryanodine receptor 2 by calmodulin. Nature (2019)

Release Date

2019-07-17

Peptides

RyR2: ADGJ
Peptidyl-prolyl cis-trans isomerase FKBP1B: BEHK
Calmodulin-1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

Membrane

We predict this structure to be a membrane protein.
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RyR2

Peptidyl-prolyl cis-trans isomerase FKBP1B

Calmodulin-1

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