SMTL ID : 6jiy.1

Structure of RyR2 (F/A/C/H-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: 4 residues within 4Å: Chain A: C.4889, 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.9: 4 residues within 4Å: Chain D: C.4889, C.4892, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.4889, D:C.4892, D:H.4909 ZN.17: 4 residues within 4Å: Chain G: C.4889, 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 ZN.25: 4 residues within 4Å: Chain J: C.4889, C.4892, H.4909, H.4914 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.4889, J:C.4892, J:H.4909

20 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 4 residues within 4Å: Chain A: E.3849, E.3923, T.4932, E.4933 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.3849, A:E.3849, A:E.3923, A:T.4932 CA.5: 6 residues within 4Å: Chain C: D.21, D.23, T.27, I.28, T.29, E.32 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.23, C:D.23, C:T.27, C:E.32, C:E.32 CA.6: 5 residues within 4Å: Chain C: D.59, N.61, T.63, I.64, D.65 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.59, C:T.63, C:T.63 CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.8: 6 residues within 4Å: Chain C: D.130, I.131, D.132, D.134, N.138, E.141 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.130, C:D.134, C:D.134 CA.10: 4 residues within 4Å: Chain D: E.3849, E.3923, T.4932, E.4933 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.3849, D:E.3849, D:E.3923, D:T.4932 CA.13: 6 residues within 4Å: Chain F: D.21, D.23, T.27, I.28, T.29, E.32 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.23, F:D.23, F:T.27, F:E.32, F:E.32 CA.14: 5 residues within 4Å: Chain F: D.59, N.61, T.63, I.64, D.65 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.59, F:T.63, F:T.63 CA.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 6 residues within 4Å: Chain F: D.130, I.131, D.132, D.134, N.138, E.141 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.130, F:D.134, F:D.134 CA.18: 4 residues within 4Å: Chain G: E.3849, E.3923, T.4932, E.4933 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3849, G:E.3849, G:E.3923, G:T.4932 CA.21: 6 residues within 4Å: Chain I: D.21, D.23, T.27, I.28, T.29, E.32 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.23, I:D.23, I:T.27, I:E.32, I:E.32 CA.22: 5 residues within 4Å: Chain I: D.59, N.61, T.63, I.64, D.65 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.59, I:T.63, I:T.63 CA.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.24: 6 residues within 4Å: Chain I: D.130, I.131, D.132, D.134, N.138, E.141 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.130, I:D.134, I:D.134 CA.26: 4 residues within 4Å: Chain J: E.3849, E.3923, T.4932, E.4933 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:E.3849, J:E.3849, J:E.3923, J:T.4932 CA.29: 6 residues within 4Å: Chain L: D.21, D.23, T.27, I.28, T.29, E.32 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:D.23, L:D.23, L:T.27, L:E.32, L:E.32 CA.30: 5 residues within 4Å: Chain L: D.59, N.61, T.63, I.64, D.65 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.59, L:T.63, L:T.63 CA.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.32: 6 residues within 4Å: Chain L: D.130, I.131, D.132, D.134, N.138, E.141 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:D.130, L:D.134, L:D.134

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

ATP.3: 10 residues within 4Å: Chain A: K.4167, K.4170, R.4171, K.4882, M.4885, C.4889, F.4890, T.4910, N.4915, L.4916 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.4890, A:L.4916 Salt bridges: A:K.4167, A:K.4170, A:K.4170, A:R.4171, A:K.4882 ATP.11: 10 residues within 4Å: Chain D: K.4167, K.4170, R.4171, K.4882, M.4885, C.4889, F.4890, T.4910, N.4915, L.4916 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:F.4890, D:L.4916 Salt bridges: D:K.4167, D:K.4170, D:K.4170, D:R.4171, D:K.4882 ATP.19: 10 residues within 4Å: Chain G: K.4167, K.4170, R.4171, K.4882, M.4885, C.4889, F.4890, T.4910, N.4915, L.4916 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:F.4890, G:L.4916 Salt bridges: G:K.4167, G:K.4170, G:K.4170, G:R.4171, G:K.4882 ATP.27: 10 residues within 4Å: Chain J: K.4167, K.4170, R.4171, K.4882, M.4885, C.4889, F.4890, T.4910, N.4915, L.4916 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:F.4890, J:L.4916 Salt bridges: J:K.4167, J:K.4170, J:K.4170, J:R.4171, J:K.4882

4 x CFF: CAFFEINE(Non-covalent)

CFF.4: 6 residues within 4Å: Chain A: I.4198, W.4646, I.4927, W.4942, Y.4945, Q.4946 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:W.4646, A:W.4646, A:W.4646 CFF.12: 6 residues within 4Å: Chain D: I.4198, W.4646, I.4927, W.4942, Y.4945, Q.4946 3 PLIP interactions: 3 interactions with chain D pi-Stacking: D:W.4646, D:W.4646, D:W.4646 CFF.20: 6 residues within 4Å: Chain G: I.4198, W.4646, I.4927, W.4942, Y.4945, Q.4946 3 PLIP interactions: 3 interactions with chain G pi-Stacking: G:W.4646, G:W.4646, G:W.4646 CFF.28: 6 residues within 4Å: Chain J: I.4198, W.4646, I.4927, W.4942, Y.4945, Q.4946 3 PLIP interactions: 3 interactions with chain J 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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