SMTL ID : 8sgi.1

Cryo-EM structure of human NCX1 in complex with SEA0400

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x EKY: 2-{4-[(2,5-difluorophenyl)methoxy]phenoxy}-5-ethoxyaniline(Non-covalent)

EKY.1: 17 residues within 4Å: Chain A: E.132, V.134, L.137, T.138, H.200, V.203, V.206, T.207, W.210, C.245, F.248, A.249, L.257, D.839, A.840, G.843, G.847 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.134, A:V.134, A:L.137, A:L.137, A:V.206, A:W.210, A:L.257, A:D.839, A:D.839 Hydrogen bonds: A:T.138, A:C.245

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: I.221, I.225, S.226, V.229, E.234 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:I.221, A:I.225, A:S.226, A:E.234, A:E.234 CA.3: 4 residues within 4Å: Chain A: N.131, E.277, D.587, E.589 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.277, A:E.277, A:D.587, A:E.589 CA.4: 3 residues within 4Å: Chain A: D.431, E.461, E.464 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.431, A:D.431, A:E.461, A:E.464, A:E.464 CA.5: 3 residues within 4Å: Chain A: E.395, D.431, E.461 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.395, A:D.431, A:E.461 CA.6: 5 residues within 4Å: Chain A: E.395, D.456, D.457, D.509, D.510 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.395, A:D.456, A:D.509, A:D.510, A:D.510 CA.7: 6 residues within 4Å: Chain A: E.395, D.457, I.459, E.461, D.508, D.510 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.395, A:D.457, A:I.459, A:E.461, A:D.510

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

NA.8: 6 residues within 4Å: Chain A: S.144, S.145, P.147, E.148, T.820, D.824 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.820 NA.9: 5 residues within 4Å: Chain A: E.148, S.174, A.817, T.820, S.821 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.148, A:T.820 NA.10: 5 residues within 4Å: Chain A: A.141, S.144, S.145, D.824, S.848 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.824

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, J. et al., Structural mechanisms of human cardiac sodium calcium exchanger NCX1. To Be Published

Release Date

2024-04-24

Peptides

Sodium/calcium exchanger 1: A
Fab light chain: B
Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

C
H

Membrane

We predict this structure to be a membrane protein.
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Sodium/calcium exchanger 1

Fab light chain

Fab heavy chain

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