SMTL ID : 7a0y.2 (3 other biounits)

Structure of dimeric sodium proton antiporter NhaA K300R variant, at pH 8.2, crystallized with chimeric Fab antibodies

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 15 residues within 4Å: Chain A: R.209, T.210, G.211, I.214, L.215, R.255, L.256, L.260 Chain B: I.214, R.255, L.256, V.259, W.263, I.268 Ligands: 3PE.5 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.214, B:W.263, B:I.268, A:I.214, A:L.215, A:L.256, A:L.260 Salt bridges: B:R.255, B:R.255, A:R.209, A:R.255 Hydrogen bonds: A:G.211

3 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.2: 7 residues within 4Å: Chain A: V.207, R.208, R.209, V.212, L.215 Chain B: P.262, W.263 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.262, B:W.263, B:W.263, A:L.215 Hydrogen bonds: A:R.208, A:R.209 Salt bridges: A:R.209 3PH.6: 10 residues within 4Å: Chain B: V.55, L.58, I.60, S.185, V.187, S.188, V.191, T.222, A.223, K.226 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.55, B:I.60, B:V.191, B:V.191, B:A.223 Hydrogen bonds: B:S.185 Salt bridges: B:K.226, B:K.226 3PH.7: 6 residues within 4Å: Chain A: P.262, W.263 Chain B: V.207, R.208, R.209, L.215 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.215, A:W.263, A:W.263 Hydrogen bonds: B:R.208, B:R.209 Salt bridges: B:R.208, B:R.209

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: K.85, N.203, I.242, P.243, L.244, K.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.203, A:I.242, A:L.244, A:K.245 Salt bridges: A:K.85 PO4.8: 5 residues within 4Å: Chain B: K.85, N.203, P.243, L.244, K.245 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.203, B:L.244, B:K.245 Salt bridges: B:K.85

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 10 residues within 4Å: Chain A: Q.282, G.283, V.284, E.361, N.364, W.365, L.368 Chain D: G.23, K.61, G.63 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.61 PG4.9: 10 residues within 4Å: Chain B: Q.282, G.283, V.284, E.361, N.364, W.365, L.368 Chain F: G.23, K.61, G.63 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:K.61, B:N.364

1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.5: 10 residues within 4Å: Chain A: V.259, L.260, W.263, I.268 Chain B: R.209, T.210, G.211, L.215, R.255 Ligands: CDL.1 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.215, A:L.260, A:I.268 Hydrogen bonds: B:T.210, B:G.211, B:R.255, B:R.255 Salt bridges: B:R.209

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

CL.10: 2 residues within 4Å: Chain C: R.80, Q.82 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: R.59, Y.60, K.65 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: E.46, W.47 Chain D: I.93, F.94 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain E: E.46, W.47 Chain F: I.93, F.94 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fippel, A. et al., Molecular determinants for substrate uptake in electrogenic sodium/proton antiporters. To Be Published

Release Date

2022-02-23

Peptides

Na(+)/H(+) antiporter NhaA: AB
chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain: CE
chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

Membrane

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

chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain

chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain

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