SMTL ID : 7tkt.1

SthK closed state, cAMP-bound in the presence of detergent

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

CMP.1: 8 residues within 4Å: Chain A: I.348, F.385, G.386, E.387, M.388, R.396, T.397, A.398 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.386, A:E.387, A:E.387, A:M.388, A:T.397, A:A.398 Salt bridges: A:R.396 CMP.15: 8 residues within 4Å: Chain B: I.348, F.385, G.386, E.387, M.388, R.396, T.397, A.398 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.386, B:E.387, B:E.387, B:M.388, B:T.397, B:A.398 Salt bridges: B:R.396 CMP.29: 8 residues within 4Å: Chain C: I.348, F.385, G.386, E.387, M.388, R.396, T.397, A.398 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.386, C:E.387, C:E.387, C:M.388, C:T.397, C:A.398 Salt bridges: C:R.396 CMP.49: 8 residues within 4Å: Chain D: I.348, F.385, G.386, E.387, M.388, R.396, T.397, A.398 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.386, D:E.387, D:E.387, D:M.388, D:T.397, D:A.398 Salt bridges: D:R.396

52 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: 14 residues within 4Å: Chain A: L.53, V.54, L.119, P.120, S.121, L.134, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.3, PGW.4, PGW.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.53, A:L.134, A:F.162, A:L.177 Hydrogen bonds: A:L.119, A:S.121, A:S.176 PGW.3: 10 residues within 4Å: Chain A: A.166, L.177, P.213, T.214, V.217, V.221, L.225 Ligands: PGW.2, PGW.5, PGW.43 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.166, A:L.177, A:V.217, A:V.221, A:L.225 PGW.4: 1 residues within 4Å: Ligands: PGW.2 No protein-ligand interaction detected (PLIP) PGW.5: 4 residues within 4Å: Chain A: P.122, L.125 Ligands: PGW.2, PGW.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.122, A:L.125 PGW.6: 4 residues within 4Å: Chain A: L.134, A.141, S.158, F.162 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.134, A:L.134, A:A.141, A:F.162, A:F.162 PGW.7: 4 residues within 4Å: Chain A: F.162, L.232 Ligands: PGW.8, PGW.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.162, A:L.232 PGW.8: 3 residues within 4Å: Chain A: A.228 Ligands: PGW.7, PGW.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.228 PGW.9: 3 residues within 4Å: Chain A: G.186, F.193 Ligands: PGW.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.193 PGW.10: 4 residues within 4Å: Chain A: L.51, H.168, A.185, Y.189 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.185, A:Y.189 PGW.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGW.12: 2 residues within 4Å: Chain A: L.51, L.58 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.58 PGW.13: 12 residues within 4Å: Chain A: L.156, V.160, L.200, T.201, I.237, L.240 Chain B: L.224, A.228, L.232 Ligands: PGW.14, PGW.21, PGW.22 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.156, A:V.160, A:T.201, A:I.237, A:L.240, B:L.224 PGW.14: 2 residues within 4Å: Chain A: L.157 Ligands: PGW.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.157 PGW.16: 14 residues within 4Å: Chain B: L.53, V.54, L.119, P.120, S.121, L.134, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.17, PGW.18, PGW.19 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.53, B:L.134, B:F.162, B:L.177 Hydrogen bonds: B:L.119, B:S.121, B:S.176 PGW.17: 10 residues within 4Å: Chain B: A.166, L.177, P.213, T.214, V.217, V.221, L.225 Ligands: PGW.9, PGW.16, PGW.19 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.166, B:L.177, B:V.217, B:V.221, B:L.225 PGW.18: 1 residues within 4Å: Ligands: PGW.16 No protein-ligand interaction detected (PLIP) PGW.19: 4 residues within 4Å: Chain B: P.122, L.125 Ligands: PGW.16, PGW.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.122, B:L.125 PGW.20: 4 residues within 4Å: Chain B: L.134, A.141, S.158, F.162 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.134, B:L.134, B:A.141, B:F.162, B:F.162 PGW.21: 4 residues within 4Å: Chain B: F.162, L.232 Ligands: PGW.13, PGW.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.162, B:L.232 PGW.22: 3 residues within 4Å: Chain B: A.228 Ligands: PGW.13, PGW.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.228 PGW.23: 4 residues within 4Å: Chain B: G.186, F.193 Ligands: PGW.25, PGW.31 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.193 PGW.24: 4 residues within 4Å: Chain B: L.51, H.168, A.185, Y.189 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.185, B:Y.189 PGW.25: 1 residues within 4Å: Ligands: PGW.23 No protein-ligand interaction detected (PLIP) PGW.26: 2 residues within 4Å: Chain B: L.51, L.58 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.58 PGW.27: 12 residues within 4Å: Chain B: L.156, V.160, L.200, T.201, I.237, L.240 Chain C: L.224, A.228, L.232 Ligands: PGW.28, PGW.35, PGW.36 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.156, B:V.160, B:T.201, B:I.237, B:L.240, C:L.224 PGW.28: 2 residues within 4Å: Chain B: L.157 Ligands: PGW.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.157 PGW.30: 14 residues within 4Å: Chain C: L.53, V.54, L.119, P.120, S.121, L.134, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.31, PGW.32, PGW.33 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.53, C:L.134, C:F.162, C:L.177 Hydrogen bonds: C:L.119, C:S.121, C:S.176 PGW.31: 10 residues within 4Å: Chain C: A.166, L.177, P.213, T.214, V.217, V.221, L.225 Ligands: PGW.23, PGW.30, PGW.33 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.166, C:L.177, C:V.217, C:V.221, C:L.225 PGW.32: 1 residues within 4Å: Ligands: PGW.30 No protein-ligand interaction detected (PLIP) PGW.33: 4 residues within 4Å: Chain C: P.122, L.125 Ligands: PGW.30, PGW.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.122, C:L.125 PGW.34: 4 residues within 4Å: Chain C: L.134, A.141, S.158, F.162 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.134, C:L.134, C:A.141, C:F.162, C:F.162 PGW.35: 4 residues within 4Å: Chain C: F.162, L.232 Ligands: PGW.27, PGW.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.162, C:L.232 PGW.36: 3 residues within 4Å: Chain C: A.228 Ligands: PGW.27, PGW.35 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.228 PGW.37: 4 residues within 4Å: Chain C: G.186, F.193 Ligands: PGW.39, PGW.51 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.193 PGW.38: 4 residues within 4Å: Chain C: L.51, H.168, A.185, Y.189 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.185, C:Y.189 PGW.39: 1 residues within 4Å: Ligands: PGW.37 No protein-ligand interaction detected (PLIP) PGW.40: 2 residues within 4Å: Chain C: L.51, L.58 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.58 PGW.41: 12 residues within 4Å: Chain C: L.156, V.160, L.200, T.201, I.237, L.240 Chain D: L.224, A.228, L.232 Ligands: PGW.42, PGW.55, PGW.56 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.156, C:V.160, C:T.201, C:I.237, C:L.240, D:L.224 PGW.42: 2 residues within 4Å: Chain C: L.157 Ligands: PGW.41 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.157 PGW.43: 4 residues within 4Å: Chain D: G.186, F.193 Ligands: PGW.3, PGW.45 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.193 PGW.44: 4 residues within 4Å: Chain D: L.51, H.168, A.185, Y.189 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.185, D:Y.189 PGW.45: 1 residues within 4Å: Ligands: PGW.43 No protein-ligand interaction detected (PLIP) PGW.46: 2 residues within 4Å: Chain D: L.51, L.58 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.58 PGW.47: 12 residues within 4Å: Chain A: L.224, A.228, L.232 Chain D: L.156, V.160, L.200, T.201, I.237, L.240 Ligands: PGW.7, PGW.8, PGW.48 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.156, D:V.160, D:T.201, D:I.237, D:L.240, A:L.224 PGW.48: 2 residues within 4Å: Chain D: L.157 Ligands: PGW.47 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.157 PGW.50: 14 residues within 4Å: Chain D: L.53, V.54, L.119, P.120, S.121, L.134, F.162, G.169, G.173, S.176, L.177 Ligands: PGW.51, PGW.52, PGW.53 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.53, D:L.134, D:F.162, D:L.177 Hydrogen bonds: D:L.119, D:S.121, D:S.176 PGW.51: 10 residues within 4Å: Chain D: A.166, L.177, P.213, T.214, V.217, V.221, L.225 Ligands: PGW.37, PGW.50, PGW.53 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.166, D:L.177, D:V.217, D:V.221, D:L.225 PGW.52: 1 residues within 4Å: Ligands: PGW.50 No protein-ligand interaction detected (PLIP) PGW.53: 4 residues within 4Å: Chain D: P.122, L.125 Ligands: PGW.50, PGW.51 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:P.122, D:L.125 PGW.54: 4 residues within 4Å: Chain D: L.134, A.141, S.158, F.162 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.134, D:L.134, D:A.141, D:F.162, D:F.162 PGW.55: 4 residues within 4Å: Chain D: F.162, L.232 Ligands: PGW.41, PGW.56 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.162, D:L.232 PGW.56: 3 residues within 4Å: Chain D: A.228 Ligands: PGW.41, PGW.55 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidpeter, P.A.M. et al., Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-10-26

Peptides

Putative transcriptional regulator, Crp/Fnr family: 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.
Show / Hide

Putative transcriptional regulator, Crp/Fnr family

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