SMTL ID : 7rys.1

SthK R120A Open State 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)

CMP.1: 12 residues within 4Å: Chain A: V.367, Y.376, F.385, G.386, E.387, M.388, A.389, R.396, T.397, A.398, R.437, E.439 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.386, A:E.387, A:E.387, A:A.389, A:R.396, A:T.397, A:R.437, A:E.439 CMP.9: 12 residues within 4Å: Chain B: V.367, Y.376, F.385, G.386, E.387, M.388, A.389, R.396, T.397, A.398, R.437, E.439 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.386, B:E.387, B:E.387, B:A.389, B:R.396, B:T.397, B:R.437, B:E.439 CMP.17: 12 residues within 4Å: Chain C: V.367, Y.376, F.385, G.386, E.387, M.388, A.389, R.396, T.397, A.398, R.437, E.439 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.386, C:E.387, C:E.387, C:A.389, C:R.396, C:T.397, C:R.437, C:E.439 CMP.25: 12 residues within 4Å: Chain D: V.367, Y.376, F.385, G.386, E.387, M.388, A.389, R.396, T.397, A.398, R.437, E.439 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.386, D:E.387, D:E.387, D:A.389, D:R.396, D:T.397, D:R.437, D:E.439

28 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

PGW.2: 9 residues within 4Å: Chain A: G.186, T.187, Y.189, L.190, F.193 Chain B: P.213, T.214, V.217 Ligands: PGW.4 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.217, B:V.217, A:Y.189, A:L.190, A:L.190, A:F.193, A:F.193 PGW.3: 6 residues within 4Å: Chain A: L.51, L.164, H.168, A.185, Y.189 Ligands: PGW.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.51, A:A.185, A:Y.189, A:Y.189 PGW.4: 1 residues within 4Å: Ligands: PGW.2 No protein-ligand interaction detected (PLIP) PGW.5: 5 residues within 4Å: Chain A: Y.44, I.47, L.51, L.58 Ligands: PGW.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.44, A:I.47 PGW.6: 6 residues within 4Å: Chain A: I.163, L.164, I.237 Chain B: L.224, A.228, L.232 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.224, B:A.228, B:L.232, A:I.163, A:L.164, A:I.237 PGW.7: 5 residues within 4Å: Chain A: L.53, S.121, L.125, G.169, S.176 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.53 PGW.8: 2 residues within 4Å: Chain A: T.214, V.221 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.221 PGW.10: 9 residues within 4Å: Chain B: G.186, T.187, Y.189, L.190, F.193 Chain C: P.213, T.214, V.217 Ligands: PGW.12 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.189, B:L.190, B:L.190, B:F.193, B:F.193, C:V.217, C:V.217 PGW.11: 6 residues within 4Å: Chain B: L.51, L.164, H.168, A.185, Y.189 Ligands: PGW.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.51, B:A.185, B:Y.189, B:Y.189 PGW.12: 1 residues within 4Å: Ligands: PGW.10 No protein-ligand interaction detected (PLIP) PGW.13: 5 residues within 4Å: Chain B: Y.44, I.47, L.51, L.58 Ligands: PGW.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.44, B:I.47 PGW.14: 5 residues within 4Å: Chain B: I.163, L.164, I.237 Chain C: A.228, L.232 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.163, B:L.164, B:I.237, C:A.228, C:L.232 PGW.15: 5 residues within 4Å: Chain B: L.53, S.121, L.125, G.169, S.176 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.53 PGW.16: 2 residues within 4Å: Chain B: T.214, V.221 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.221 PGW.18: 12 residues within 4Å: Chain C: G.186, T.187, Y.189, L.190, F.193 Chain D: P.213, T.214, V.217, I.220, V.221, L.224 Ligands: PGW.20 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.189, C:L.190, C:L.190, C:F.193, C:F.193, D:V.217, D:V.217, D:I.220, D:L.224 PGW.19: 6 residues within 4Å: Chain C: L.51, L.164, H.168, A.185, Y.189 Ligands: PGW.21 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.51, C:A.185, C:Y.189, C:Y.189 PGW.20: 1 residues within 4Å: Ligands: PGW.18 No protein-ligand interaction detected (PLIP) PGW.21: 5 residues within 4Å: Chain C: Y.44, I.47, L.51, L.58 Ligands: PGW.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.44, C:I.47 PGW.22: 6 residues within 4Å: Chain C: I.163, L.164, I.237 Chain D: L.224, A.228, L.232 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.224, D:A.228, D:L.232, C:I.163, C:L.164, C:I.237 PGW.23: 5 residues within 4Å: Chain C: L.53, S.121, L.125, G.169, S.176 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.53 PGW.24: 2 residues within 4Å: Chain C: T.214, V.221 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.221 PGW.26: 9 residues within 4Å: Chain A: P.213, T.214, V.217 Chain D: G.186, T.187, Y.189, L.190, F.193 Ligands: PGW.28 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.189, D:L.190, D:L.190, D:F.193, D:F.193, A:V.217, A:V.217 PGW.27: 6 residues within 4Å: Chain D: L.51, L.164, H.168, A.185, Y.189 Ligands: PGW.29 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.51, D:A.185, D:Y.189, D:Y.189 PGW.28: 1 residues within 4Å: Ligands: PGW.26 No protein-ligand interaction detected (PLIP) PGW.29: 5 residues within 4Å: Chain D: Y.44, I.47, L.51, L.58 Ligands: PGW.27 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.44, D:I.47 PGW.30: 4 residues within 4Å: Chain A: L.232 Chain D: I.163, L.164, I.237 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:I.163, D:L.164, D:I.237, A:L.232 PGW.31: 5 residues within 4Å: Chain D: L.53, S.121, L.125, G.169, S.176 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.53 PGW.32: 2 residues within 4Å: Chain D: T.214, V.221 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, X. et al., Gating intermediates reveal inhibitory role of the voltage sensor in a cyclic nucleotide-modulated ion channel. Nat Commun (2022)

Release Date

2022-11-23

Peptides

SthK: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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SthK

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