SMTL ID : 5jdg.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 0.1mM Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

2 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.51 NA.2: 5 residues within 4Å: Chain A: T.50, S.51, E.54, T.209, E.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.213

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

1PE.3: 7 residues within 4Å: Chain A: Y.17, S.20, D.21, M.215, L.218, A.219, K.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.222 1PE.5: 5 residues within 4Å: Chain A: S.124, W.125, S.249, M.252, H.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.125, A:S.249 1PE.6: 1 residues within 4Å: Chain A: R.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.282 1PE.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: R.140, V.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.140

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

OLC.8: 7 residues within 4Å: Chain A: S.37, N.38, N.224, L.225, G.226, G.227, M.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.38, A:G.226, A:G.227, A:M.228 OLC.9: 2 residues within 4Å: Chain A: Y.60, E.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.180 OLC.10: 7 residues within 4Å: Chain A: V.117, I.118, I.120, D.121, D.127 Ligands: MYS.17, CA.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.121, A:D.127

16 x MYS: PENTADECANE(Non-covalent)

MYS.11: 4 residues within 4Å: Chain A: Q.260, I.296, L.299, M.301 Ligand excluded by PLIP MYS.12: 2 residues within 4Å: Chain A: W.125, L.250 Ligand excluded by PLIP MYS.13: 4 residues within 4Å: Chain A: V.107, F.114, L.134 Ligands: MYS.16 Ligand excluded by PLIP MYS.14: 5 residues within 4Å: Chain A: V.259, L.291, S.298, R.300 Ligands: MYS.15 Ligand excluded by PLIP MYS.15: 3 residues within 4Å: Chain A: I.294, S.298 Ligands: MYS.14 Ligand excluded by PLIP MYS.16: 6 residues within 4Å: Chain A: L.110, I.113, F.114, V.117, I.118 Ligands: MYS.13 Ligand excluded by PLIP MYS.17: 4 residues within 4Å: Chain A: F.114, I.126, D.127 Ligands: OLC.10 Ligand excluded by PLIP MYS.18: 2 residues within 4Å: Chain A: L.109, Y.272 Ligand excluded by PLIP MYS.19: 3 residues within 4Å: Chain A: A.116, I.120, N.258 Ligand excluded by PLIP MYS.20: 4 residues within 4Å: Chain A: T.44, V.45, I.48, V.143 Ligand excluded by PLIP MYS.21: 1 residues within 4Å: Chain A: R.282 Ligand excluded by PLIP MYS.22: 1 residues within 4Å: Chain A: L.270 Ligand excluded by PLIP MYS.23: 1 residues within 4Å: Chain A: F.274 Ligand excluded by PLIP MYS.24: 1 residues within 4Å: Chain A: Y.60 Ligand excluded by PLIP MYS.25: 3 residues within 4Å: Chain A: A.59, Y.60, Y.63 Ligand excluded by PLIP MYS.26: 2 residues within 4Å: Chain A: L.13, Y.17 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.27: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.10 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

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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