SMTL ID : 9cgp.1

RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.4958, A:C.4961, A:H.4983 ZN.4: 4 residues within 4Å: Chain B: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.4958, B:C.4961, B:H.4983 ZN.7: 4 residues within 4Å: Chain C: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.4958, C:C.4961, C:H.4983 ZN.10: 4 residues within 4Å: Chain D: C.4958, C.4961, H.4978, H.4983 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.4958, D:C.4961, D:H.4983

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

ATP.2: 11 residues within 4Å: Chain A: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.4984, A:L.4985 Salt bridges: A:K.4214, A:K.4214, A:R.4215 ATP.5: 11 residues within 4Å: Chain B: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.4984, B:L.4985 Salt bridges: B:K.4214, B:K.4214, B:R.4215 ATP.8: 11 residues within 4Å: Chain C: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.4984, C:L.4985 Salt bridges: C:K.4214, C:K.4214, C:R.4215 ATP.11: 11 residues within 4Å: Chain D: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, T.4979, H.4983, N.4984, L.4985 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.4984, D:L.4985 Salt bridges: D:K.4214, D:K.4214, D:R.4215

4 x U1C: Dantrolene(Non-covalent)

U1C.3: 6 residues within 4Å: Chain A: W.882, H.904, N.921, M.924, W.996, S.1038 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.882, A:W.882, A:W.882, A:W.996, A:W.996 U1C.6: 8 residues within 4Å: Chain B: W.882, H.904, E.917, N.921, M.924, W.996, R.1000, S.1038 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.882, B:W.882, B:E.917 Hydrogen bonds: B:R.1000 pi-Stacking: B:W.882 U1C.9: 7 residues within 4Å: Chain C: W.882, H.904, E.917, N.921, M.924, W.996, S.1038 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.882, C:W.882, C:W.882, C:E.917, C:W.996 U1C.12: 7 residues within 4Å: Chain D: W.882, R.897, H.904, N.921, M.924, W.996, S.1038 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.882, D:W.882 Hydrogen bonds: D:R.897

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iyer, K.A. et al., Manuscript in preparation. To Be Published

Release Date

2024-12-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Ryanodine receptor 1

Peptidyl-prolyl cis-trans isomerase FKBP1B

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