SMTL ID : 8u71.1

Structure of sea urchin SLC9C1 at pH 8 in Na+

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

POV.1: 7 residues within 4Å: Chain A: D.134, V.137, Q.140, W.353 Ligands: AJP.2, AJP.3, POV.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.137, A:V.137, A:W.353 Hydrogen bonds: A:D.134 POV.4: 7 residues within 4Å: Chain A: M.355 Ligands: POV.1, AJP.2, AJP.3, POV.5, AJP.6, AJP.7 No protein-ligand interaction detected (PLIP) POV.5: 7 residues within 4Å: Chain B: D.134, V.137, Q.140, Y.309 Ligands: POV.4, AJP.6, AJP.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.137, B:Y.309

4 x AJP: Digitonin

AJP.2: 9 residues within 4Å: Chain A: K.76, V.77, D.129, F.142, L.356, L.359 Ligands: POV.1, POV.4, AJP.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.77, A:V.77, A:F.142, A:F.142, A:L.356, A:L.359 Salt bridges: A:K.76 AJP.3: 10 residues within 4Å: Chain A: H.136, Q.140, L.305, Y.309 Chain B: I.78, I.81, L.359 Ligands: POV.1, POV.4, AJP.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.305, B:I.78, B:I.81, B:L.359 Hydrogen bonds: A:Q.140 AJP.6: 10 residues within 4Å: Chain A: I.78, I.81, L.359 Chain B: H.136, Q.140, L.305, Y.309 Ligands: AJP.2, POV.4, POV.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.305, A:I.78, A:I.81, A:L.359 Hydrogen bonds: B:Q.140 AJP.7: 12 residues within 4Å: Chain B: K.76, V.77, D.129, M.133, I.141, F.142, L.356, L.359, L.363 Ligands: AJP.3, POV.4, POV.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.77, B:V.77, B:I.141, B:F.142, B:L.356, B:L.359, B:L.363 Hydrogen bonds: B:K.76, B:D.129 Salt bridges: B:K.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, S. et al., SLC9C1 at pH 8 in presence of K+. To Be Published

Release Date

2025-03-26

Peptides

Sperm-specific sodium proton exchanger: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sperm-specific sodium proton exchanger

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