SMTL ID : 5tan.1

Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

ATP.1: 9 residues within 4Å: Chain E: K.3850, R.3854, M.4333, C.4337, I.4339, F.4354, T.4358, N.4363, L.4364 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.3854, E:H.4362 Salt bridges: E:K.3850, E:K.3850, E:K.3850, E:K.3853, E:R.3854 ATP.5: 9 residues within 4Å: Chain F: K.3850, R.3854, M.4333, C.4337, I.4339, F.4354, T.4358, N.4363, L.4364 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.3854, F:H.4362 Salt bridges: F:K.3850, F:K.3850, F:K.3850, F:K.3853, F:R.3854 ATP.9: 9 residues within 4Å: Chain G: K.3850, R.3854, M.4333, C.4337, I.4339, F.4354, T.4358, N.4363, L.4364 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:R.3854, G:H.4362 Salt bridges: G:K.3850, G:K.3850, G:K.3850, G:K.3853, G:R.3854 ATP.13: 9 residues within 4Å: Chain H: K.3850, R.3854, M.4333, C.4337, I.4339, F.4354, T.4358, N.4363, L.4364 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:R.3854, H:H.4362 Salt bridges: H:K.3850, H:K.3850, H:K.3850, H:K.3853, H:R.3854

4 x CFF: CAFFEINE(Non-covalent)

CFF.2: 6 residues within 4Å: Chain E: E.3878, I.3881, W.4095, I.4375, W.4390, Y.4393 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.3878 pi-Stacking: E:W.4095, E:W.4095, E:W.4095 CFF.6: 6 residues within 4Å: Chain F: E.3878, I.3881, W.4095, I.4375, W.4390, Y.4393 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.3878 pi-Stacking: F:W.4095, F:W.4095, F:W.4095 CFF.10: 6 residues within 4Å: Chain G: E.3878, I.3881, W.4095, I.4375, W.4390, Y.4393 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:E.3878 pi-Stacking: G:W.4095, G:W.4095, G:W.4095 CFF.14: 6 residues within 4Å: Chain H: E.3878, I.3881, W.4095, I.4375, W.4390, Y.4393 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.3878 pi-Stacking: H:W.4095, H:W.4095, H:W.4095

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain E: C.4337, I.4339, C.4340, H.4357, H.4362 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.4337, E:C.4340, E:H.4357, E:H.4362 ZN.7: 5 residues within 4Å: Chain F: C.4337, I.4339, C.4340, H.4357, H.4362 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4337, F:C.4340, F:H.4357, F:H.4362 ZN.11: 5 residues within 4Å: Chain G: C.4337, I.4339, C.4340, H.4357, H.4362 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4337, G:C.4340, G:H.4357, G:H.4362 ZN.15: 5 residues within 4Å: Chain H: C.4337, I.4339, C.4340, H.4357, H.4362 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4337, H:C.4340, H:H.4357, H:H.4362

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain E: E.3532, E.3606, Q.3609, T.4380, E.4381, H.4382 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.3532, E:E.3606, E:T.4380 CA.8: 6 residues within 4Å: Chain F: E.3532, E.3606, Q.3609, T.4380, E.4381, H.4382 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.3532, F:E.3606, F:T.4380 CA.12: 6 residues within 4Å: Chain G: E.3532, E.3606, Q.3609, T.4380, E.4381, H.4382 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.3532, G:E.3606, G:T.4380 CA.16: 6 residues within 4Å: Chain H: E.3532, E.3606, Q.3609, T.4380, E.4381, H.4382 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.3532, H:E.3606, H:T.4380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

des Georges, A. et al., Structural Basis for Gating and Activation of RyR1. Cell (2016)

Release Date

2016-10-12

Peptides

Peptidyl-prolyl cis-trans isomerase FKBP1B: ABCD
Ryanodine receptor 1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
A

C
H

D
J

E
B

F
E

G
I

H
G

Membrane

We predict this structure to be a membrane protein.
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Peptidyl-prolyl cis-trans isomerase FKBP1B

Ryanodine receptor 1

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