SMTL ID : 5hwy.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 zero Ca2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

OLC.1: 7 residues within 4Å: Chain A: T.203, L.204, F.207, Y.292 Ligands: MYS.5, MYS.6, MYS.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.203, A:L.204, A:F.207

2 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.50 Water bridges: A:N.81 NA.3: 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

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

MYS.4: 2 residues within 4Å: Chain A: L.193 Ligands: MYS.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.193 MYS.5: 3 residues within 4Å: Ligands: OLC.1, MYS.4, ACT.19 No protein-ligand interaction detected (PLIP) MYS.6: 4 residues within 4Å: Chain A: L.88, F.207, L.218 Ligands: OLC.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.88, A:F.207, A:F.207, A:L.218 MYS.7: 3 residues within 4Å: Chain A: L.10, Y.18 Ligands: MYS.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.10 MYS.8: 3 residues within 4Å: Chain A: W.125, L.132, L.250 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.125, A:L.132 MYS.9: 4 residues within 4Å: Chain A: I.113, A.116, V.117, N.258 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.113, A:A.116, A:V.117, A:N.258 MYS.10: 2 residues within 4Å: Chain A: Y.17 Ligands: MYS.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.17, A:Y.17 MYS.11: 1 residues within 4Å: Chain A: F.251 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.251 MYS.12: 5 residues within 4Å: Chain A: G.76, Q.260, L.299, R.300 Ligands: OLC.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.299, A:L.299 MYS.13: 2 residues within 4Å: Chain A: W.283, Q.284 No protein-ligand interaction detected (PLIP) MYS.14: 2 residues within 4Å: Chain A: I.30, L.165 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.30, A:L.165 MYS.15: 2 residues within 4Å: Chain A: V.45, I.48 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.45, A:I.48 MYS.16: 7 residues within 4Å: Chain A: V.263, L.291, I.294, A.295, S.298, L.299 Ligands: MYS.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.263, A:L.291, A:I.294, A:L.299 MYS.17: 1 residues within 4Å: Ligands: MYS.16 No protein-ligand interaction detected (PLIP) MYS.18: 2 residues within 4Å: Chain A: S.298, R.300 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.300

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.19: 1 residues within 4Å: Ligands: MYS.5 No protein-ligand interaction detected (PLIP)

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

1PE.20: 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

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

2016-05-18

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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