SMTL ID : 9gsf.1

Mouse PMCA-NPTN complex captured in E1-ATP state without calcium

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 18 residues within 4Å: Chain A: K.455, T.456, N.522, T.524, E.525, F.557, K.562, S.563, M.564, K.580, A.582, R.625, I.627, T.686, G.687, D.688, R.745 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.522, A:E.525, A:E.525, A:R.625, A:R.625, A:T.686, A:G.687, A:G.687, A:G.687, A:D.688, A:R.745 Salt bridges: A:R.625 pi-Stacking: A:F.557

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ANP.1 No protein-ligand interaction detected (PLIP)

1 x KXP: (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl icosa-5,8,11,14-tetraenoate(Non-covalent)

KXP.3: 13 residues within 4Å: Chain A: L.348, Q.351, I.352, A.355, G.356, M.359, A.409, L.838, N.841, V.842, V.845, P.900, I.902 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.355, A:V.845 Hydrogen bonds: A:Q.351, A:Q.351, A:I.902

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 4 residues within 4Å: Chain B: N.316, S.323, A.324, S.325 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.323 NAG.5: 2 residues within 4Å: Chain B: K.259, N.295 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.259 NAG.6: 5 residues within 4Å: Chain B: N.283, G.286, F.288, F.289, I.290 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.290 Hydrogen bonds: B:N.283, B:F.288 NAG.7: 3 residues within 4Å: Chain B: N.170, N.199, E.201 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain B: T.184, H.216, N.228 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.216 Hydrogen bonds: B:H.216 NAG.9: 4 residues within 4Å: Chain B: L.178, M.179, Y.180, N.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.178, B:L.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

vinayagam, D. et al., Cryo-EM structure of PMCA-NPTN complex captured in E1-ATP state. To Be Published

Release Date

2025-08-06

Peptides

Plasma membrane calcium-transporting ATPase 2: A
Neuroplastin: B

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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Plasma membrane calcium-transporting ATPase 2

Neuroplastin

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