SMTL ID : 7rsh.1

SthK Y26F Closed State

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

CMP.1: 9 residues within 4Å: Chain A: Y.376, A.377, F.385, G.386, E.387, M.388, R.396, T.397, A.398 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.386, A:E.387, A:E.387, A:T.397 Salt bridges: A:R.396 CMP.16: 9 residues within 4Å: Chain B: Y.376, A.377, F.385, G.386, E.387, M.388, R.396, T.397, A.398 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.386, B:E.387, B:E.387, B:T.397 Salt bridges: B:R.396 CMP.31: 9 residues within 4Å: Chain C: Y.376, A.377, F.385, G.386, E.387, M.388, R.396, T.397, A.398 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.386, C:E.387, C:E.387, C:T.397 Salt bridges: C:R.396 CMP.47: 9 residues within 4Å: Chain D: Y.376, A.377, F.385, G.386, E.387, M.388, R.396, T.397, A.398 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.386, D:E.387, D:E.387, D:T.397 Salt bridges: D:R.396

56 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: 10 residues within 4Å: Chain A: G.186, Y.189 Chain B: T.212, P.213, T.214, V.217, I.220, L.224 Ligands: PGW.3, PGW.6 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.217, B:I.220, B:L.224, A:Y.189 Hydrogen bonds: B:T.214 PGW.3: 4 residues within 4Å: Ligands: PGW.2, PGW.5, PGW.6, PGW.7 No protein-ligand interaction detected (PLIP) PGW.4: 4 residues within 4Å: Chain A: I.47, A.185, Y.189 Ligands: PGW.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.47, A:A.185, A:Y.189, A:Y.189 PGW.5: 6 residues within 4Å: Chain A: Y.44, I.47, L.51, L.58 Ligands: PGW.3, PGW.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.44, A:I.47, A:L.51, A:L.58 PGW.6: 3 residues within 4Å: Ligands: PGW.2, PGW.3, PGW.7 No protein-ligand interaction detected (PLIP) PGW.7: 2 residues within 4Å: Ligands: PGW.3, PGW.6 No protein-ligand interaction detected (PLIP) PGW.8: 7 residues within 4Å: Chain A: L.156, V.160, I.237, L.240 Chain B: A.227, A.228, L.232 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.227, B:A.228, B:L.232, A:L.156, A:V.160, A:I.237, A:L.240 PGW.9: 3 residues within 4Å: Chain A: L.153, L.157, V.160 No protein-ligand interaction detected (PLIP) PGW.10: 11 residues within 4Å: Chain A: L.53, S.121, L.128, L.131, L.134, F.162, L.165, A.166, G.169, G.173, S.176 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.53, A:L.128, A:L.134, A:F.162, A:L.165, A:A.166 PGW.11: 4 residues within 4Å: Chain A: L.125, S.176, Y.218 Ligands: PGW.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.218 PGW.12: 4 residues within 4Å: Chain A: T.214, Y.218, V.221 Ligands: PGW.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.221 PGW.13: 1 residues within 4Å: Chain A: P.122 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.122 PGW.14: 6 residues within 4Å: Chain A: L.125, L.128, L.131, L.132, I.135, F.162 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.128, A:L.131, A:F.162 PGW.15: 4 residues within 4Å: Chain A: R.252 Chain B: N.150, L.153, L.157 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.157 PGW.17: 10 residues within 4Å: Chain B: G.186, Y.189 Chain C: T.212, P.213, T.214, V.217, I.220, L.224 Ligands: PGW.18, PGW.21 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.189, C:V.217, C:I.220, C:L.224 Hydrogen bonds: C:T.214 PGW.18: 4 residues within 4Å: Ligands: PGW.17, PGW.20, PGW.21, PGW.22 No protein-ligand interaction detected (PLIP) PGW.19: 4 residues within 4Å: Chain B: I.47, A.185, Y.189 Ligands: PGW.20 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.47, B:A.185, B:Y.189, B:Y.189 PGW.20: 6 residues within 4Å: Chain B: Y.44, I.47, L.51, L.58 Ligands: PGW.18, PGW.19 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.44, B:I.47, B:L.51, B:L.58 PGW.21: 3 residues within 4Å: Ligands: PGW.17, PGW.18, PGW.22 No protein-ligand interaction detected (PLIP) PGW.22: 2 residues within 4Å: Ligands: PGW.18, PGW.21 No protein-ligand interaction detected (PLIP) PGW.23: 7 residues within 4Å: Chain B: L.156, V.160, I.237, L.240 Chain C: A.227, A.228, L.232 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.227, C:A.228, C:L.232, B:L.156, B:V.160, B:I.237, B:L.240 PGW.24: 3 residues within 4Å: Chain B: L.153, L.157, V.160 No protein-ligand interaction detected (PLIP) PGW.25: 11 residues within 4Å: Chain B: L.53, S.121, L.128, L.131, L.134, F.162, L.165, A.166, G.169, G.173, S.176 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.53, B:L.128, B:L.134, B:F.162, B:L.165, B:A.166 PGW.26: 4 residues within 4Å: Chain B: L.125, S.176, Y.218 Ligands: PGW.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.218 PGW.27: 4 residues within 4Å: Chain B: T.214, Y.218, V.221 Ligands: PGW.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.221 PGW.28: 1 residues within 4Å: Chain B: P.122 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.122 PGW.29: 6 residues within 4Å: Chain B: L.125, L.128, L.131, L.132, I.135, F.162 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.128, B:L.131, B:F.162 PGW.30: 4 residues within 4Å: Chain B: R.252 Chain C: N.150, L.153, L.157 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.157 PGW.32: 10 residues within 4Å: Chain C: G.186, Y.189 Chain D: T.212, P.213, T.214, V.217, I.220, L.224 Ligands: PGW.33, PGW.36 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.217, D:I.220, D:L.224, C:Y.189 Hydrogen bonds: D:T.214 PGW.33: 3 residues within 4Å: Ligands: PGW.32, PGW.35, PGW.37 No protein-ligand interaction detected (PLIP) PGW.34: 4 residues within 4Å: Chain C: I.47, A.185, Y.189 Ligands: PGW.35 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.47, C:A.185, C:Y.189, C:Y.189 PGW.35: 6 residues within 4Å: Chain C: Y.44, I.47, L.51, L.58 Ligands: PGW.33, PGW.34 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.44, C:I.47, C:L.51, C:L.58 PGW.36: 2 residues within 4Å: Ligands: PGW.32, PGW.37 No protein-ligand interaction detected (PLIP) PGW.37: 2 residues within 4Å: Ligands: PGW.33, PGW.36 No protein-ligand interaction detected (PLIP) PGW.38: 7 residues within 4Å: Chain C: L.156, V.160, I.237, L.240 Chain D: A.227, A.228, L.232 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.227, D:A.228, D:L.232, C:L.156, C:V.160, C:I.237, C:L.240 PGW.39: 3 residues within 4Å: Chain C: L.153, L.157, V.160 No protein-ligand interaction detected (PLIP) PGW.40: 11 residues within 4Å: Chain C: L.53, S.121, L.128, L.131, L.134, F.162, L.165, A.166, G.169, G.173, S.176 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.53, C:L.128, C:L.134, C:F.162, C:L.165, C:A.166 PGW.41: 4 residues within 4Å: Chain C: L.125, S.176, Y.218 Ligands: PGW.42 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.218 PGW.42: 4 residues within 4Å: Chain C: T.214, Y.218, V.221 Ligands: PGW.41 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.221 PGW.43: 1 residues within 4Å: Chain C: P.122 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.122 PGW.44: 6 residues within 4Å: Chain C: L.125, L.128, L.131, L.132, I.135, F.162 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.128, C:L.131, C:F.162 PGW.45: 4 residues within 4Å: Chain C: R.252 Chain D: N.150, L.153, L.157 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.157 PGW.46: 4 residues within 4Å: Chain A: N.150, L.153, L.157 Chain D: R.252 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.157 PGW.48: 10 residues within 4Å: Chain A: T.212, P.213, T.214, V.217, I.220, L.224 Chain D: G.186, Y.189 Ligands: PGW.49, PGW.52 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:V.217, A:I.220, A:L.224, D:Y.189 Hydrogen bonds: A:T.214 PGW.49: 4 residues within 4Å: Ligands: PGW.48, PGW.51, PGW.52, PGW.53 No protein-ligand interaction detected (PLIP) PGW.50: 4 residues within 4Å: Chain D: I.47, A.185, Y.189 Ligands: PGW.51 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.47, D:A.185, D:Y.189, D:Y.189 PGW.51: 6 residues within 4Å: Chain D: Y.44, I.47, L.51, L.58 Ligands: PGW.49, PGW.50 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.44, D:I.47, D:L.51, D:L.58 PGW.52: 3 residues within 4Å: Ligands: PGW.48, PGW.49, PGW.53 No protein-ligand interaction detected (PLIP) PGW.53: 2 residues within 4Å: Ligands: PGW.49, PGW.52 No protein-ligand interaction detected (PLIP) PGW.54: 7 residues within 4Å: Chain A: A.227, A.228, L.232 Chain D: L.156, V.160, I.237, L.240 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.156, D:V.160, D:I.237, D:L.240, A:A.227, A:A.228, A:L.232 PGW.55: 3 residues within 4Å: Chain D: L.153, L.157, V.160 No protein-ligand interaction detected (PLIP) PGW.56: 11 residues within 4Å: Chain D: L.53, S.121, L.128, L.131, L.134, F.162, L.165, A.166, G.169, G.173, S.176 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.53, D:L.128, D:L.134, D:F.162, D:L.165, D:A.166 PGW.57: 4 residues within 4Å: Chain D: L.125, S.176, Y.218 Ligands: PGW.58 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.218 PGW.58: 4 residues within 4Å: Chain D: T.214, Y.218, V.221 Ligands: PGW.57 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.221 PGW.59: 1 residues within 4Å: Chain D: P.122 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.122 PGW.60: 6 residues within 4Å: Chain D: L.125, L.128, L.131, L.132, I.135, F.162 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.128, D:L.131, D:F.162

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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