SMTL ID : 5hxs.1

Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 10mM Sr2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.1: 5 residues within 4Å: Chain A: T.50, S.51, E.54, T.209, E.213 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.50, A:E.54, A:E.54, A:T.209, A:E.213 SR.2: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.118, A:D.121, A:G.122, A:D.127, H2O.1

7 x MYS: PENTADECANE(Non-covalent)

MYS.3: 1 residues within 4Å: Chain A: F.207 No protein-ligand interaction detected (PLIP) MYS.4: 5 residues within 4Å: Chain A: F.274, S.278, W.283, Q.284, L.287 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.274, A:L.287 MYS.5: 1 residues within 4Å: Chain A: V.45 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.45 MYS.6: 6 residues within 4Å: Chain A: V.263, I.266, L.291, S.298, L.299 Ligands: MYS.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.263, A:V.263, A:I.266, A:L.291, A:L.299 MYS.7: 2 residues within 4Å: Chain A: L.270 Ligands: MYS.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.270 MYS.8: 2 residues within 4Å: Chain A: W.125, L.250 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.125, A:W.125, A:L.250, A:L.250 MYS.9: 2 residues within 4Å: Chain A: I.14, Y.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.14, A:Y.18

1 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.10: 7 residues within 4Å: Chain A: Y.17, S.20, D.21, M.215, L.218, A.219, K.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.21, A:K.222

2 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.11: 7 residues within 4Å: Chain A: L.110, F.114, V.117, I.118, D.121, D.127 Ligands: SR.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.114, A:F.114, A:V.117, A:V.117 Hydrogen bonds: A:D.127 OLC.12: 7 residues within 4Å: Chain A: S.37, N.38, N.224, L.225, G.226, G.227, M.228 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.38, A:N.224, A:G.226, A:G.227, A:M.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liao, J. et al., Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-05-11

Peptides

sodium,calcium exchanger: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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sodium,calcium exchanger

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