SMTL ID : 9gsd.1

Cryo-EM structure of mouse PMCA-NPTN complex captured in E2 state (BEF3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.04 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.454, T.456, D.775 Ligands: BEF.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.454, A:T.456, A:D.775

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.2: 13 residues within 4Å: Chain A: Q.351, I.352, A.355, M.359, A.409, L.838, N.841, V.842, V.845, P.900, I.902, M.907, I.910 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.355, A:V.842 Hydrogen bonds: A:Q.351, A:Q.351, A:I.902

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 9 residues within 4Å: Chain A: S.239, G.243, D.454, T.456, T.686, G.687, K.751, N.778 Ligands: MG.1 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain B: N.283, 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.5: 7 residues within 4Å: Chain B: R.271, E.314, N.316, T.318, S.323, A.324, S.325 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.271, B:R.271, B:E.314, B:T.318, B:S.323, B:S.325 NAG.6: 5 residues within 4Å: Chain B: T.240, K.259, V.261, E.294, N.295 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.240, B:K.259 Hydrogen bonds: B:N.295 NAG.7: 3 residues within 4Å: Chain B: N.170, N.199, E.201 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.199 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 mouse PMCA-NPTN complex captured in E1 state without calcium. 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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