SMTL ID : 7tzc.1

A drug and ATP binding site in type 1 ryanodine receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.22, A:D.26, A:T.28, A:E.33, A:E.33 CA.2: 6 residues within 4Å: Chain A: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.58, A:D.60, A:T.64, A:E.69, A:E.69 CA.3: 5 residues within 4Å: Chain A: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.95, A:D.97, A:Y.101, A:E.106, A:E.106 CA.4: 6 residues within 4Å: Chain A: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.131, A:D.135, A:Q.137, A:E.142, A:E.142 CA.5: 5 residues within 4Å: Chain C: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.22, C:D.26, C:T.28, C:E.33, C:E.33 CA.6: 6 residues within 4Å: Chain C: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.58, C:D.60, C:T.64, C:E.69, C:E.69 CA.7: 5 residues within 4Å: Chain C: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.95, C:D.97, C:Y.101, C:E.106, C:E.106 CA.8: 6 residues within 4Å: Chain C: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.131, C:D.135, C:Q.137, C:E.142, C:E.142 CA.9: 5 residues within 4Å: Chain D: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.22, D:D.26, D:T.28, D:E.33, D:E.33 CA.10: 6 residues within 4Å: Chain D: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:D.60, D:T.64, D:E.69, D:E.69 CA.11: 5 residues within 4Å: Chain D: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.95, D:D.97, D:Y.101, D:E.106, D:E.106 CA.12: 6 residues within 4Å: Chain D: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.131, D:D.135, D:Q.137, D:E.142, D:E.142 CA.13: 5 residues within 4Å: Chain E: D.22, D.24, D.26, T.28, E.33 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.22, E:D.26, E:T.28, E:E.33, E:E.33 CA.14: 6 residues within 4Å: Chain E: D.58, D.60, N.62, T.64, D.66, E.69 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.58, E:D.60, E:T.64, E:E.69, E:E.69 CA.15: 5 residues within 4Å: Chain E: D.95, D.97, N.99, Y.101, E.106 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.95, E:D.97, E:Y.101, E:E.106, E:E.106 CA.16: 6 residues within 4Å: Chain E: D.131, D.133, D.135, Q.137, N.139, E.142 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.131, E:D.135, E:Q.137, E:E.142, E:E.142 CA.18: 3 residues within 4Å: Chain F: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.3893, F:E.3967, F:E.3967, F:T.5001 CA.26: 3 residues within 4Å: Chain G: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.3893, G:E.3967, G:E.3967, G:T.5001 CA.35: 3 residues within 4Å: Chain H: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:E.3893, H:E.3967, H:E.3967, H:T.5001 CA.43: 3 residues within 4Å: Chain I: E.3893, E.3967, T.5001 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:E.3893, I:E.3967, I:E.3967, I:T.5001

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

ATP.17: 14 residues within 4Å: Chain F: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:F.4959, F:I.4960, F:T.4979, F:H.4983, F:L.4985 Salt bridges: F:K.4211, F:K.4211, F:K.4214, F:K.4214, F:K.4214, F:R.4215 ATP.21: 11 residues within 4Å: Chain F: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.22 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.886, F:N.921, F:H.993, F:R.1000, F:N.1018, F:N.1035 Salt bridges: F:R.897, F:R.1020 pi-Stacking: F:W.996 ATP.25: 14 residues within 4Å: Chain G: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:F.4959, G:I.4960, G:T.4979, G:H.4983, G:L.4985 Salt bridges: G:K.4211, G:K.4211, G:K.4214, G:K.4214, G:K.4214, G:R.4215 ATP.29: 11 residues within 4Å: Chain G: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.30 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:R.886, G:N.921, G:H.993, G:R.1000, G:N.1018, G:N.1035 Salt bridges: G:R.897, G:R.1020 pi-Stacking: G:W.996 ATP.34: 14 residues within 4Å: Chain H: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:F.4959, H:I.4960, H:T.4979, H:H.4983, H:L.4985 Salt bridges: H:K.4211, H:K.4211, H:K.4214, H:K.4214, H:K.4214, H:R.4215 ATP.38: 11 residues within 4Å: Chain H: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.39 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:R.886, H:N.921, H:H.993, H:R.1000, H:N.1018, H:N.1035 Salt bridges: H:R.897, H:R.1020 pi-Stacking: H:W.996 ATP.42: 14 residues within 4Å: Chain I: K.4211, K.4214, R.4215, M.4954, E.4955, K.4957, C.4958, F.4959, I.4960, F.4975, T.4979, H.4983, N.4984, L.4985 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:F.4959, I:I.4960, I:T.4979, I:H.4983, I:L.4985 Salt bridges: I:K.4211, I:K.4211, I:K.4214, I:K.4214, I:K.4214, I:R.4215 ATP.46: 11 residues within 4Å: Chain I: R.886, R.897, D.899, N.921, M.924, H.993, W.996, R.1000, R.1020, N.1035 Ligands: KVR.47 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:R.886, I:N.921, I:H.993, I:R.1000, I:N.1018, I:N.1035 Salt bridges: I:R.897, I:R.1020 pi-Stacking: I:W.996

4 x ZN: ZINC ION(Non-covalent)

ZN.19: 4 residues within 4Å: Chain F: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.4958, F:C.4961, F:H.4978, F:H.4983 ZN.27: 4 residues within 4Å: Chain G: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.4958, G:C.4961, G:H.4978, G:H.4983 ZN.36: 4 residues within 4Å: Chain H: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.4958, H:C.4961, H:H.4978, H:H.4983 ZN.44: 4 residues within 4Å: Chain I: C.4958, C.4961, H.4978, H.4983 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.4958, I:C.4961, I:H.4978, I:H.4983

4 x CFF: CAFFEINE(Non-covalent)

CFF.20: 5 residues within 4Å: Chain F: F.3753, E.4239, W.4716, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.4239 pi-Stacking: F:W.4716, F:W.4716, F:W.4716 CFF.28: 5 residues within 4Å: Chain G: F.3753, E.4239, W.4716, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:E.4239 pi-Stacking: G:W.4716, G:W.4716, G:W.4716 CFF.37: 5 residues within 4Å: Chain H: F.3753, E.4239, W.4716, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:E.4239 pi-Stacking: H:W.4716, H:W.4716, H:W.4716 CFF.45: 5 residues within 4Å: Chain I: F.3753, E.4239, W.4716, I.4996, W.5011 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:E.4239 pi-Stacking: I:W.4716, I:W.4716, I:W.4716

4 x KVR: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid(Non-covalent)

KVR.22: 10 residues within 4Å: Chain F: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.21 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:W.882, F:Y.920 Hydrogen bonds: F:E.917 Salt bridges: F:H.879, F:H.904 pi-Cation interactions: F:W.882 KVR.30: 10 residues within 4Å: Chain G: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.29 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:W.882, G:Y.920 Hydrogen bonds: G:E.917 Salt bridges: G:H.879, G:H.904 pi-Cation interactions: G:W.882 KVR.39: 10 residues within 4Å: Chain H: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.38 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:W.882, H:Y.920 Hydrogen bonds: H:E.917 Salt bridges: H:H.879, H:H.904 pi-Cation interactions: H:W.882 KVR.47: 10 residues within 4Å: Chain I: H.879, W.882, H.904, C.906, L.913, E.917, R.918, Y.920, N.921 Ligands: ATP.46 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:W.882, I:Y.920 Hydrogen bonds: I:E.917 Salt bridges: I:H.879, I:H.904 pi-Cation interactions: I:W.882

8 x L9R: (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

L9R.23: 13 residues within 4Å: Chain F: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Chain H: Y.4630, N.4805 Ligands: L9R.33 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.4847, F:L.4850, F:Y.4851, F:Y.4851, F:F.4858, F:F.4858, F:F.4859, F:Y.4912, F:F.4916, F:F.4923 Hydrogen bonds: F:Y.4909 L9R.24: 14 residues within 4Å: Chain F: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Chain G: L.4850, V.4853, N.4857, F.4858 Ligands: L9R.31 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:V.4797, F:L.4801, F:L.4801, F:F.4808, F:A.4811, F:L.4814, G:L.4850, G:V.4853, G:F.4858 Hydrogen bonds: F:N.4805 L9R.31: 13 residues within 4Å: Chain F: Y.4630, N.4805 Chain G: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Ligands: L9R.24 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:V.4847, G:L.4850, G:Y.4851, G:Y.4851, G:F.4858, G:F.4858, G:F.4859, G:Y.4912, G:F.4916, G:F.4923 Hydrogen bonds: G:Y.4909 L9R.32: 14 residues within 4Å: Chain G: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Chain I: L.4850, V.4853, N.4857, F.4858 Ligands: L9R.48 9 PLIP interactions: 3 interactions with chain I, 6 interactions with chain G Hydrophobic interactions: I:L.4850, I:V.4853, I:F.4858, G:V.4797, G:L.4801, G:L.4801, G:A.4811, G:L.4814 Hydrogen bonds: G:N.4805 L9R.33: 14 residues within 4Å: Chain F: L.4850, V.4853, N.4857, F.4858 Chain H: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Ligands: L9R.23 9 PLIP interactions: 6 interactions with chain H, 3 interactions with chain F Hydrophobic interactions: H:V.4797, H:L.4801, H:L.4801, H:A.4811, H:L.4814, F:L.4850, F:V.4853, F:F.4858 Hydrogen bonds: H:N.4805 L9R.40: 13 residues within 4Å: Chain H: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Chain I: Y.4630, N.4805 Ligands: L9R.41 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:V.4847, H:L.4850, H:Y.4851, H:Y.4851, H:F.4858, H:F.4858, H:F.4859, H:Y.4912, H:F.4916, H:F.4923 Hydrogen bonds: H:Y.4909 L9R.41: 14 residues within 4Å: Chain H: L.4850, V.4853, N.4857, F.4858 Chain I: W.4794, V.4797, L.4801, Y.4804, N.4805, F.4807, F.4808, A.4811, L.4814 Ligands: L9R.40 10 PLIP interactions: 7 interactions with chain I, 3 interactions with chain H Hydrophobic interactions: I:V.4797, I:L.4801, I:L.4801, I:F.4808, I:A.4811, I:L.4814, H:L.4850, H:V.4853, H:F.4858 Hydrogen bonds: I:N.4805 L9R.48: 13 residues within 4Å: Chain G: Y.4630, N.4805 Chain I: V.4847, L.4850, Y.4851, N.4857, F.4858, F.4859, Y.4909, Y.4912, F.4916, F.4923 Ligands: L9R.32 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:V.4847, I:L.4850, I:Y.4851, I:Y.4851, I:F.4858, I:F.4858, I:F.4859, I:Y.4912, I:F.4916, I:F.4923 Hydrogen bonds: I:Y.4909

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melville, Z. et al., A drug and ATP binding site in type 1 ryanodine receptor. Structure (2022)

Release Date

2022-05-18

Peptides

Calmodulin-1: ACDE
Peptidyl-prolyl cis-trans isomerase FKBP1A: BJKL
Ryanodine receptor 1: FGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
D

D
E

E
C

B
F

J
H

K
J

L
O

F
A

G
B

H
G

I
I

Membrane

We predict this structure to be a membrane protein.
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Calmodulin-1

Peptidyl-prolyl cis-trans isomerase FKBP1A

Ryanodine receptor 1

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