SMTL ID : 6ji0.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.4889, A:C.4892, A:H.4909 ZN.5: 5 residues within 4Å: Chain C: C.4889, I.4891, C.4892, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.4889, C:C.4892, C:H.4909 ZN.9: 5 residues within 4Å: Chain E: C.4889, I.4891, C.4892, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.4889, E:C.4892, E:H.4909 ZN.13: 5 residues within 4Å: Chain G: C.4889, I.4891, C.4892, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.4889, G:C.4892, G:H.4909

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

ATP.2: 11 residues within 4Å: Chain A: K.4167, K.4170, R.4171, M.4885, E.4886, C.4889, F.4890, I.4891, F.4906, 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.4167, A:K.4170, A:K.4170, A:R.4171 ATP.6: 11 residues within 4Å: Chain C: K.4167, K.4170, R.4171, M.4885, E.4886, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:F.4890, C:T.4910 Salt bridges: C:K.4167, C:K.4167, C:K.4170, C:K.4170, C:R.4171 ATP.10: 11 residues within 4Å: Chain E: K.4167, K.4170, R.4171, M.4885, E.4886, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:F.4890, E:T.4910 Salt bridges: E:K.4167, E:K.4167, E:K.4170, E:K.4170, E:R.4171 ATP.14: 11 residues within 4Å: Chain G: K.4167, K.4170, R.4171, M.4885, E.4886, C.4889, F.4890, I.4891, F.4906, 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.4167, G:K.4170, G:K.4170, G:R.4171

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: Q.3845, E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3849, A:E.3849, A:E.3923, A:T.4932 CA.7: 4 residues within 4Å: Chain C: Q.3845, E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.3849, C:E.3849, C:E.3923, C:T.4932 CA.11: 4 residues within 4Å: Chain E: Q.3845, E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.3849, E:E.3849, E:E.3923, E:T.4932 CA.15: 4 residues within 4Å: Chain G: Q.3845, E.3849, E.3923, T.4932 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3849, G:E.3849, G:E.3923, G:T.4932

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain A: F.3715, I.4198, W.4646, I.4927, W.4942, Y.4945 4 PLIP interactions: 4 interactions with chain A pi-Stacking: A:W.4646, A:W.4646, A:W.4646, A:W.4646 CFF.8: 6 residues within 4Å: Chain C: F.3715, I.4198, W.4646, I.4927, W.4942, Y.4945 4 PLIP interactions: 4 interactions with chain C pi-Stacking: C:W.4646, C:W.4646, C:W.4646, C:W.4646 CFF.12: 6 residues within 4Å: Chain E: F.3715, I.4198, W.4646, I.4927, W.4942, Y.4945 4 PLIP interactions: 4 interactions with chain E pi-Stacking: E:W.4646, E:W.4646, E:W.4646, E:W.4646 CFF.16: 6 residues within 4Å: Chain G: F.3715, I.4198, W.4646, I.4927, W.4942, Y.4945 4 PLIP interactions: 4 interactions with chain G pi-Stacking: G:W.4646, G:W.4646, G:W.4646, G: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: ACEG
Peptidyl-prolyl cis-trans isomerase FKBP1B: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Membrane

We predict this structure to be a membrane protein.
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RyR2

Peptidyl-prolyl cis-trans isomerase FKBP1B

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