SMTL ID : 5bz3.1

CRYSTAL STRUCTURE OF SODIUM PROTON ANTIPORTER NAPA IN OUTWARD-FACING CONFORMATION.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

14 x 7E8: (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE(Non-covalent)

7E8.1: 15 residues within 4Å: Chain A: E.51, E.56, S.126, F.271, V.275, R.278, L.279, R.330, G.331, E.332, L.335, L.356, V.359, V.360, T.363 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.278, A:L.335, A:V.359 Hydrogen bonds: A:R.278 Water bridges: A:R.278 Salt bridges: A:R.278 7E8.2: 14 residues within 4Å: Chain A: E.34, M.69, E.73, R.132, Q.135, E.136, L.140, S.141, R.251, F.261, E.264, S.265, A.268, P.269 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.73, A:E.73, A:Q.135 Hydrogen bonds: A:Q.135, A:E.264 Salt bridges: A:R.132 7E8.3: 11 residues within 4Å: Chain A: K.24, N.27, V.30, E.136, L.137, V.139, K.371, I.374, A.375, E.378, R.379 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.137, A:R.379 Hydrogen bonds: A:N.27, A:E.136 Salt bridges: A:K.371 7E8.4: 15 residues within 4Å: Chain A: R.182, L.183, L.186, L.197, L.221, G.224, M.225, A.227, L.228, S.231, I.232 Chain B: L.7, F.10, Y.11 Ligands: 7E8.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.221, B:F.10, B:F.10 Hydrogen bonds: A:R.182, A:R.182, A:S.231 7E8.5: 7 residues within 4Å: Chain A: G.178, T.181, R.182, V.185, L.186 Ligands: 7E8.4, 7E8.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.182 7E8.6: 6 residues within 4Å: Chain A: F.87, I.184, V.185, V.188, V.189 Ligands: 7E8.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.184, A:V.188, A:V.189 7E8.7: 6 residues within 4Å: Chain A: V.18, F.21, I.22, R.25 Chain B: R.208, P.210 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.210, A:V.18, A:F.21, A:I.22 Hydrogen bonds: B:R.208, A:R.25, A:R.25 7E8.8: 15 residues within 4Å: Chain B: E.51, E.56, S.126, F.271, V.275, R.278, L.279, R.330, G.331, E.332, L.335, L.356, V.359, V.360, T.363 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.278, B:L.335, B:V.359 Hydrogen bonds: B:R.278 Water bridges: B:R.278 Salt bridges: B:R.278 7E8.9: 14 residues within 4Å: Chain B: E.34, M.69, E.73, R.132, Q.135, E.136, L.140, S.141, R.251, F.261, E.264, S.265, A.268, P.269 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.73, B:E.73, B:Q.135 Hydrogen bonds: B:Q.135, B:E.264 Salt bridges: B:R.132 7E8.10: 11 residues within 4Å: Chain B: K.24, N.27, V.30, E.136, L.137, V.139, K.371, I.374, A.375, E.378, R.379 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.137, B:R.379 Hydrogen bonds: B:N.27, B:E.136, B:E.136 Salt bridges: B:K.371 7E8.11: 15 residues within 4Å: Chain A: L.7, F.10, Y.11 Chain B: R.182, L.183, L.186, L.197, L.221, G.224, M.225, A.227, L.228, S.231, I.232 Ligands: 7E8.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.221, A:F.10, A:F.10 Hydrogen bonds: B:R.182, B:R.182, B:S.231 7E8.12: 7 residues within 4Å: Chain B: G.178, T.181, R.182, V.185, L.186 Ligands: 7E8.11, 7E8.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.182 7E8.13: 6 residues within 4Å: Chain B: F.87, I.184, V.185, V.188, V.189 Ligands: 7E8.12 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.184, B:V.188, B:V.189 7E8.14: 6 residues within 4Å: Chain A: R.208, P.210 Chain B: V.18, F.21, I.22, R.25 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.210, B:V.18, B:F.21, B:I.22 Hydrogen bonds: A:R.208, B:R.25, B:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coincon, M. et al., Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-01-20

Peptides

Na(+)/H(+) antiporter: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Na(+)/H(+) antiporter