SMTL ID : 5jdn.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: A.47, T.50, S.51, E.213, S.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.50 Water bridges: A:N.81

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

SR.2: 5 residues within 4Å: Chain A: T.50, S.51, E.54, T.209, E.213 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.50, A:E.54, A:T.209, A:E.213, H2O.1 SR.3: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:I.118, A:D.121, A:G.122, A:D.127

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

OLC.4: 7 residues within 4Å: Chain A: F.114, V.117, I.118, D.121, I.126, D.127 Ligands: SR.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.114, A:F.114, A:F.114, A:V.117, A:I.118 Hydrogen bonds: A:I.118, A:D.121 OLC.5: 7 residues within 4Å: Chain A: S.37, N.38, N.224, L.225, G.226, G.227, M.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.38, A:N.38, A:N.224, A:L.225, A:G.227, A:M.228

5 x MYS: PENTADECANE(Non-covalent)

MYS.6: 2 residues within 4Å: Chain A: W.125, L.250 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.250, A:L.250, A:L.250 MYS.7: 4 residues within 4Å: Chain A: V.107, L.110, F.111, L.134 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.107, A:L.134 MYS.8: 2 residues within 4Å: Chain A: L.291, I.294 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.291, A:I.294 MYS.9: 4 residues within 4Å: Chain A: L.106, L.109, L.110, L.269 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.106, A:L.109, A:L.110, A:L.269 MYS.10: 2 residues within 4Å: Chain A: I.120, N.258 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.120, A:N.258

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.11: 7 residues within 4Å: Chain A: Y.17, S.20, D.21, M.215, L.218, A.219, K.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.17, A:S.20, A:K.222 1PE.12: 5 residues within 4Å: Chain A: P.53, L.56, L.176, A.179, E.180 No protein-ligand interaction detected (PLIP)

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 NCX_Mj: 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 NCX_Mj

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