SMTL ID : 7rtf.1

SthK R120A Closed State

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

CMP.1: 7 residues within 4Å: Chain A: 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:T.397, A:A.398 Salt bridges: A:R.396 CMP.14: 7 residues within 4Å: Chain B: 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:T.397, B:A.398 Salt bridges: B:R.396 CMP.27: 7 residues within 4Å: Chain C: 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:T.397, C:A.398 Salt bridges: C:R.396 CMP.40: 7 residues within 4Å: Chain D: 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:T.397, D:A.398 Salt bridges: D:R.396

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

PGW.2: 11 residues within 4Å: Chain A: G.186, Y.189, L.190, F.193 Chain B: P.213, T.214, V.217, I.220, V.221, L.224 Ligands: PGW.3 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.217, B:V.217, B:I.220, B:V.221, B:L.224, A:Y.189, A:L.190, A:F.193, A:F.193 PGW.3: 3 residues within 4Å: Chain A: G.186 Ligands: PGW.2, PGW.4 No protein-ligand interaction detected (PLIP) PGW.4: 6 residues within 4Å: Chain A: L.51, L.58, A.185, Y.189 Ligands: PGW.3, PGW.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.58, A:A.185, A:Y.189, A:Y.189, A:Y.189 PGW.5: 4 residues within 4Å: Chain A: L.43, Y.44, I.47 Ligands: PGW.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.44, A:Y.44, A:I.47 PGW.6: 9 residues within 4Å: Chain A: L.156, V.160, L.200, T.201, M.229, Y.230 Chain B: A.227, A.228, L.232 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.227, B:A.228, B:L.232, A:L.156, A:L.200, A:T.201, A:M.229, A:Y.230 PGW.7: 3 residues within 4Å: Chain A: L.153, L.157, V.160 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.153 PGW.8: 5 residues within 4Å: Chain A: R.148, I.149, N.150, L.153, L.157 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.149, A:N.150, A:L.153, A:L.157 PGW.9: 12 residues within 4Å: Chain A: P.50, L.53, L.128, L.131, L.134, F.162, A.166, G.169, G.173, S.176 Ligands: PGW.10, PGW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.50, A:L.53, A:L.128, A:L.134, A:F.162, A:A.166 PGW.10: 7 residues within 4Å: Chain A: L.125, S.176, L.177, Y.218 Ligands: PGW.9, PGW.11, PGW.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.177, A:Y.218 PGW.11: 7 residues within 4Å: Chain A: I.170, V.217, Y.218, V.221, L.225 Ligands: PGW.9, PGW.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.170, A:V.217, A:Y.218, A:V.221, A:L.225 PGW.12: 2 residues within 4Å: Chain A: P.122, L.125 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.125 PGW.13: 5 residues within 4Å: Chain A: L.128, V.129, L.131, I.135 Ligands: PGW.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.131, A:I.135 PGW.15: 11 residues within 4Å: Chain B: G.186, Y.189, L.190, F.193 Chain C: P.213, T.214, V.217, I.220, V.221, L.224 Ligands: PGW.16 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.217, C:V.217, C:I.220, C:V.221, C:L.224, B:Y.189, B:L.190, B:F.193, B:F.193 PGW.16: 3 residues within 4Å: Chain B: G.186 Ligands: PGW.15, PGW.17 No protein-ligand interaction detected (PLIP) PGW.17: 6 residues within 4Å: Chain B: L.51, L.58, A.185, Y.189 Ligands: PGW.16, PGW.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.58, B:A.185, B:Y.189, B:Y.189, B:Y.189 PGW.18: 4 residues within 4Å: Chain B: L.43, Y.44, I.47 Ligands: PGW.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.44, B:Y.44, B:I.47 PGW.19: 9 residues within 4Å: Chain B: L.156, V.160, L.200, T.201, M.229, Y.230 Chain C: A.227, A.228, L.232 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.156, B:L.200, B:T.201, B:M.229, B:Y.230, C:A.227, C:A.228, C:L.232 PGW.20: 3 residues within 4Å: Chain B: L.153, L.157, V.160 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.153 PGW.21: 5 residues within 4Å: Chain B: R.148, I.149, N.150, L.153, L.157 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.149, B:N.150, B:L.153, B:L.157 PGW.22: 12 residues within 4Å: Chain B: P.50, L.53, L.128, L.131, L.134, F.162, A.166, G.169, G.173, S.176 Ligands: PGW.23, PGW.24 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.50, B:L.53, B:L.128, B:L.134, B:F.162, B:A.166 PGW.23: 7 residues within 4Å: Chain B: L.125, S.176, L.177, Y.218 Ligands: PGW.22, PGW.24, PGW.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.177, B:Y.218 PGW.24: 7 residues within 4Å: Chain B: I.170, V.217, Y.218, V.221, L.225 Ligands: PGW.22, PGW.23 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.170, B:V.217, B:Y.218, B:V.221, B:L.225 PGW.25: 2 residues within 4Å: Chain B: P.122, L.125 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.125 PGW.26: 5 residues within 4Å: Chain B: L.128, V.129, L.131, I.135 Ligands: PGW.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.131, B:I.135 PGW.28: 11 residues within 4Å: Chain C: G.186, Y.189, L.190, F.193 Chain D: P.213, T.214, V.217, I.220, V.221, L.224 Ligands: PGW.29 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.217, D:V.217, D:I.220, D:V.221, D:L.224, C:Y.189, C:L.190, C:F.193, C:F.193 PGW.29: 3 residues within 4Å: Chain C: G.186 Ligands: PGW.28, PGW.30 No protein-ligand interaction detected (PLIP) PGW.30: 6 residues within 4Å: Chain C: L.51, L.58, A.185, Y.189 Ligands: PGW.29, PGW.31 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.58, C:A.185, C:Y.189, C:Y.189, C:Y.189 PGW.31: 4 residues within 4Å: Chain C: L.43, Y.44, I.47 Ligands: PGW.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.44, C:Y.44, C:I.47 PGW.32: 9 residues within 4Å: Chain C: L.156, V.160, L.200, T.201, M.229, Y.230 Chain D: A.227, A.228, L.232 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.156, C:L.200, C:T.201, C:M.229, C:Y.230, D:A.227, D:A.228, D:L.232 PGW.33: 3 residues within 4Å: Chain C: L.153, L.157, V.160 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.153 PGW.34: 5 residues within 4Å: Chain C: R.148, I.149, N.150, L.153, L.157 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.149, C:N.150, C:L.153, C:L.157 PGW.35: 12 residues within 4Å: Chain C: P.50, L.53, L.128, L.131, L.134, F.162, A.166, G.169, G.173, S.176 Ligands: PGW.36, PGW.37 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.50, C:L.53, C:L.128, C:L.134, C:F.162, C:A.166 PGW.36: 7 residues within 4Å: Chain C: L.125, S.176, L.177, Y.218 Ligands: PGW.35, PGW.37, PGW.39 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.177, C:Y.218 PGW.37: 7 residues within 4Å: Chain C: I.170, V.217, Y.218, V.221, L.225 Ligands: PGW.35, PGW.36 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.170, C:V.217, C:Y.218, C:V.221, C:L.225 PGW.38: 2 residues within 4Å: Chain C: P.122, L.125 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.125 PGW.39: 5 residues within 4Å: Chain C: L.128, V.129, L.131, I.135 Ligands: PGW.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.131, C:I.135 PGW.41: 11 residues within 4Å: Chain A: P.213, T.214, V.217, I.220, V.221, L.224 Chain D: G.186, Y.189, L.190, F.193 Ligands: PGW.42 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:V.217, A:V.217, A:I.220, A:V.221, A:L.224, D:Y.189, D:L.190, D:F.193, D:F.193 PGW.42: 3 residues within 4Å: Chain D: G.186 Ligands: PGW.41, PGW.43 No protein-ligand interaction detected (PLIP) PGW.43: 6 residues within 4Å: Chain D: L.51, L.58, A.185, Y.189 Ligands: PGW.42, PGW.44 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.58, D:A.185, D:Y.189, D:Y.189, D:Y.189 PGW.44: 4 residues within 4Å: Chain D: L.43, Y.44, I.47 Ligands: PGW.43 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.44, D:Y.44, D:I.47 PGW.45: 9 residues within 4Å: Chain A: A.227, A.228, L.232 Chain D: L.156, V.160, L.200, T.201, M.229, Y.230 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:A.227, A:A.228, A:L.232, D:L.156, D:L.200, D:T.201, D:M.229, D:Y.230 PGW.46: 3 residues within 4Å: Chain D: L.153, L.157, V.160 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.153 PGW.47: 5 residues within 4Å: Chain D: R.148, I.149, N.150, L.153, L.157 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.149, D:N.150, D:L.153, D:L.157 PGW.48: 12 residues within 4Å: Chain D: P.50, L.53, L.128, L.131, L.134, F.162, A.166, G.169, G.173, S.176 Ligands: PGW.49, PGW.50 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.50, D:L.53, D:L.128, D:L.134, D:F.162, D:A.166 PGW.49: 7 residues within 4Å: Chain D: L.125, S.176, L.177, Y.218 Ligands: PGW.48, PGW.50, PGW.52 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.177, D:Y.218 PGW.50: 7 residues within 4Å: Chain D: I.170, V.217, Y.218, V.221, L.225 Ligands: PGW.48, PGW.49 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:I.170, D:V.217, D:Y.218, D:V.221, D:L.225 PGW.51: 2 residues within 4Å: Chain D: P.122, L.125 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.125 PGW.52: 5 residues within 4Å: Chain D: L.128, V.129, L.131, I.135 Ligands: PGW.49 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.131, D:I.135

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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