SMTL ID : 5jdh.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 Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: N.38, L.225, G.226, G.227 Ligand excluded by PLIP

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

NA.2: 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

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.118, A:D.121, A:G.122, A:D.127, H2O.2, H2O.2 CA.4: 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:T.209, A:E.213, A:E.213

12 x MYS: PENTADECANE(Non-covalent)(Non-functional Binders)

MYS.5: 2 residues within 4Å: Chain A: L.13, Y.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.13, A:Y.17, A:Y.17 MYS.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.7: 2 residues within 4Å: Chain A: I.296, M.301 No protein-ligand interaction detected (PLIP) MYS.8: 4 residues within 4Å: Chain A: F.274, W.283, L.287, A.290 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.274, A:W.283, A:W.283, A:A.290 MYS.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.10: 3 residues within 4Å: Chain A: T.44, V.45, V.143 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.143 MYS.11: 6 residues within 4Å: Chain A: V.263, I.266, L.291, I.294, S.298 Ligands: MYS.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.263, A:I.266, A:I.294 MYS.12: 3 residues within 4Å: Chain A: L.270, L.287 Ligands: MYS.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.270, A:L.270, A:L.287 MYS.13: 3 residues within 4Å: Chain A: L.110, Y.272 Ligands: OLC.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.272 MYS.14: 5 residues within 4Å: Chain A: V.107, F.111, F.114, L.134 Ligands: OLC.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.114, A:L.134 MYS.15: 1 residues within 4Å: Chain A: Y.60 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.60 MYS.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

1PE.17: 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.18: 3 residues within 4Å: Chain A: I.118, I.126, D.127 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.127, A:D.127 1PE.20: 5 residues within 4Å: Chain A: W.125, V.129, L.132, L.250 Ligands: PEG.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.125

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.19: 5 residues within 4Å: Chain A: I.113, A.116, V.117, I.120, N.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.258

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

PEG.21: 3 residues within 4Å: Chain A: L.250, F.251 Ligands: 1PE.20 No protein-ligand interaction detected (PLIP)

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

OLC.22: 4 residues within 4Å: Chain A: F.114, V.117 Ligands: MYS.13, MYS.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.114, A:V.117 Water bridges: A:I.118, A:D.121, A:D.121, A:D.121

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

Uncharacterized membrane protein MJ0091: 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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Uncharacterized membrane protein MJ0091

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