SMTL ID : 8u7o.1

WT sea urchin SLC9C1 with 5mM cAMP at pH 6 in Na+ - Grip and Twist (GnT) conformation

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: 10 residues within 4Å: Chain A: D.134, V.137, Q.140, I.141, Y.309, Y.312, W.353 Ligands: AJP.2, POV.4, AJP.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.137, A:Y.309, A:Y.312, A:W.353 POV.4: 6 residues within 4Å: Ligands: POV.1, AJP.2, POV.5, AJP.6, AJP.7, AJP.8 No protein-ligand interaction detected (PLIP) POV.5: 8 residues within 4Å: Chain B: V.137, Q.140, I.141, Y.309, Y.312 Ligands: POV.4, AJP.7, AJP.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.137, B:Y.309, B:Y.312

4 x AJP: Digitonin

AJP.2: 8 residues within 4Å: Chain A: M.133, V.137, I.141, F.142, L.363 Ligands: POV.1, POV.4, AJP.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.137, A:I.141, A:F.142, A:L.363 Hydrogen bonds: A:K.76 Salt bridges: A:K.76, A:K.76 AJP.6: 9 residues within 4Å: Chain A: A.306, Y.309 Chain B: V.77, I.78, C.85, L.359 Ligands: POV.1, POV.4, AJP.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.309, B:V.77, B:L.359 AJP.7: 9 residues within 4Å: Chain B: K.76, V.77, V.137, I.141, F.142, L.359 Ligands: POV.4, POV.5, AJP.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.77, B:V.137, B:I.141, B:L.359 Hydrogen bonds: B:K.76 Salt bridges: B:K.76, B:K.76 AJP.8: 9 residues within 4Å: Chain A: V.77, I.78, C.85, L.359 Chain B: A.306, Y.309 Ligands: AJP.2, POV.4, POV.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.306, B:Y.309, A:V.77, A:L.359

2 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

CMP.3: 10 residues within 4Å: Chain A: L.1008, D.1034, I.1042, G.1043, E.1044, M.1045, G.1046, R.1053, N.1054, R.1097 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1043, A:E.1044, A:M.1045, A:G.1046, A:R.1097 Salt bridges: A:R.1053 CMP.9: 10 residues within 4Å: Chain B: L.1008, D.1034, I.1042, G.1043, E.1044, M.1045, G.1046, R.1053, N.1054, R.1097 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.1043, B:E.1044, B:M.1045, B:G.1046, B:N.1054, B:R.1097 Salt bridges: B:R.1053

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, S. et al., Structure of WT sp9C1 with 5mM cAMP at pH 6 in Na+ - Grip and Twist (GnT) conformation. 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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