SMTL ID : 9kcm.1

Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in (2Na+)E1-AMPPCP state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 19 residues within 4Å: Chain C: D.338, K.339, T.340, D.412, E.415, F.444, S.446, K.449, Q.451, K.470, G.471, A.472, R.513, L.515, V.578, T.579, G.580, D.581, R.654 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:D.338, C:D.338, C:D.338, C:K.339, C:T.340, C:D.412, C:D.412, C:E.415, C:S.446, C:R.513, C:T.579, C:G.580, C:G.580, C:D.581, C:R.654, C:R.654 Salt bridges: C:K.449 pi-Stacking: C:F.444, C:F.444

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain C: V.291, A.292, V.294, E.296 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.294, C:E.296 NA.3: 4 residues within 4Å: Chain C: A.292, T.741, S.744, N.745 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsui, R. et al., Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell. To Be Published

Release Date

2025-11-12

Peptides

Sodium/potassium-transporting ATPase subunit beta-3: A
Protein NDRG3: B
Sodium/potassium-transporting ATPase subunit alpha-1: C
Thioredoxin-related transmembrane protein 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
N

C
A

D
T

Membrane

We predict this structure to be a membrane protein.
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Sodium/potassium-transporting ATPase subunit beta-3

Protein NDRG3

Sodium/potassium-transporting ATPase subunit alpha-1

Thioredoxin-related transmembrane protein 2

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