SMTL ID : 5jdf.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 1mM Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.7 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 CA.2: 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

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

OLC.3: 8 residues within 4Å: Chain A: S.37, N.38, F.39, L.101, N.224, L.225, G.226, G.227 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.39, A:L.101 Hydrogen bonds: A:N.224, A:G.226, A:G.227 OLC.4: 7 residues within 4Å: Chain A: I.113, A.116, V.117, I.120, N.258, V.259, A.262 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.120, A:I.120, A:N.258, A:V.259 OLC.5: 5 residues within 4Å: Chain A: P.53, L.176, A.179, E.180, G.208 No protein-ligand interaction detected (PLIP) OLC.6: 2 residues within 4Å: Chain A: E.180, D.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.184 OLC.7: 6 residues within 4Å: Chain A: F.114, V.117, I.118, D.121, D.127 Ligands: CA.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.114, A:F.114 Hydrogen bonds: A:D.127 Water bridges: A:S.124

6 x MYS: PENTADECANE(Non-covalent)

MYS.8: 1 residues within 4Å: Chain A: L.299 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.299 MYS.9: 2 residues within 4Å: Chain A: R.140, V.143 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.140, A:V.143 MYS.10: 2 residues within 4Å: Chain A: L.291, I.294 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.291 MYS.11: 2 residues within 4Å: Chain A: W.125, L.250 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.125, A:L.250, A:L.250 MYS.12: 3 residues within 4Å: Chain A: V.107, F.114, L.134 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.107, A:F.114, A:L.134, A:L.134 MYS.13: 2 residues within 4Å: Chain A: V.259, S.298 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.259, A:V.259

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

1PE.14: 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:S.20, A:K.222

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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