SMTL ID : 6jii.1

Structure of RyR2 (F/A/C/L-Ca2+/apo-CaM-M 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 B: C.4889, I.4891, C.4892, H.4909, H.4914 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.4889, B:C.4892, B:H.4914, B:H.4914 ZN.5: 5 residues within 4Å: Chain E: C.4889, I.4891, C.4892, H.4909, H.4914 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4889, E:C.4892, E:H.4914, E:H.4914 ZN.9: 5 residues within 4Å: Chain H: C.4889, I.4891, C.4892, H.4909, H.4914 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4889, H:C.4892, H:H.4914, H:H.4914 ZN.13: 5 residues within 4Å: Chain K: C.4889, I.4891, C.4892, H.4909, H.4914 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.4889, K:C.4892, K:H.4914, K:H.4914

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain B: E.3923, Q.3926, T.4932 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.3923, B:T.4932 CA.6: 3 residues within 4Å: Chain E: E.3923, Q.3926, T.4932 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.3923, E:T.4932 CA.10: 3 residues within 4Å: Chain H: E.3923, Q.3926, T.4932 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:E.3923, H:T.4932 CA.14: 3 residues within 4Å: Chain K: E.3923, Q.3926, T.4932 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.3923, K:T.4932

4 x CFF: CAFFEINE(Non-covalent)

CFF.3: 5 residues within 4Å: Chain B: E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.4195 pi-Stacking: B:W.4646, B:W.4646, B:W.4646 CFF.7: 5 residues within 4Å: Chain E: E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.4195 pi-Stacking: E:W.4646, E:W.4646, E:W.4646 CFF.11: 5 residues within 4Å: Chain H: E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.4195 pi-Stacking: H:W.4646, H:W.4646, H:W.4646 CFF.15: 5 residues within 4Å: Chain K: E.4195, I.4198, W.4646, I.4927, Y.4945 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:E.4195 pi-Stacking: K:W.4646, K:W.4646, K:W.4646

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

ATP.4: 11 residues within 4Å: Chain B: K.4167, K.4170, R.4171, M.4885, K.4888, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.4171, B:F.4890, B:T.4910, B:L.4916 Salt bridges: B:K.4167, B:K.4167, B:K.4170, B:K.4170, B:K.4170 ATP.8: 11 residues within 4Å: Chain E: K.4167, K.4170, R.4171, M.4885, K.4888, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:F.4890, E:T.4910, E:L.4916 Salt bridges: E:K.4167, E:K.4167, E:K.4170, E:K.4170, E:K.4170, E:R.4171 ATP.12: 11 residues within 4Å: Chain H: K.4167, K.4170, R.4171, M.4885, K.4888, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:F.4890, H:T.4910, H:L.4916 Salt bridges: H:K.4167, H:K.4167, H:K.4170, H:K.4170, H:K.4170, H:R.4171 ATP.16: 11 residues within 4Å: Chain K: K.4167, K.4170, R.4171, M.4885, K.4888, C.4889, F.4890, I.4891, F.4906, T.4910, L.4916 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:F.4890, K:T.4910, K:L.4916 Salt bridges: K:K.4167, K:K.4167, K:K.4170, K:K.4170, K:K.4170, K:R.4171

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

Peptidyl-prolyl cis-trans isomerase FKBP1B: ADGJ
Ryr2: 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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Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryr2

Calmodulin-1

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