SMTL ID : 5jdl.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 Sr2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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

SR.1: 5 residues within 4Å: Chain A: I.118, D.121, G.122, D.127 Ligands: OLC.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.118, A:G.122, A:D.127, H2O.1 SR.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

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

CL.3: 4 residues within 4Å: Chain A: N.38, L.225, G.226, G.227 Ligand excluded by PLIP

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

OLC.4: 7 residues within 4Å: Chain A: I.113, V.117, I.118, D.121, D.127 Ligands: SR.1, OLC.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.117, A:V.117 Water bridges: A:S.124 OLC.5: 3 residues within 4Å: Chain A: D.121 Ligands: OLC.4, OLC.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.121 OLC.6: 1 residues within 4Å: Ligands: OLC.5 No protein-ligand interaction detected (PLIP) OLC.7: 3 residues within 4Å: Chain A: W.125, L.132, L.250 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.125, A:W.125, A:L.132, A:L.250, A:L.250

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

MYS.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MYS.9: 1 residues within 4Å: Chain A: R.140 No protein-ligand interaction detected (PLIP) MYS.10: 3 residues within 4Å: Chain A: I.113, A.116, N.258 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.113, A:A.116, A:N.258

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

1PE.11: 6 residues within 4Å: Chain A: Y.17, S.20, M.215, L.218, A.219, K.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.17, 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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