SMTL ID : 4cza.1

Structure of the sodium proton antiporter PaNhaP from Pyrococcus abyssii with bound thallium ion.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-dimer

Ligands

4 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.1: 10 residues within 4Å: Chain A: Y.31, I.69, T.72, E.73, D.130, D.295, A.298, T.302, V.364 Ligands: TL.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.69 Hydrogen bonds: A:Y.31, A:Y.31, A:E.73, A:E.73, A:D.130 TAM.4: 1 residues within 4Å: Chain B: D.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.146 TAM.5: 2 residues within 4Å: Chain B: K.281, R.285 No protein-ligand interaction detected (PLIP) TAM.6: 5 residues within 4Å: Chain B: L.167, Y.177, G.179, E.248, D.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.248, B:D.251

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 5 residues within 4Å: Chain A: E.288, K.289, H.292, D.295 Chain B: K.289 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.288 Salt bridges: A:H.292, B:K.289

2 x TL: THALLIUM (I) ION(Non-covalent)

TL.3: 5 residues within 4Å: Chain A: E.73, T.129, S.155, D.159 Ligands: TAM.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.73, A:T.129, A:S.155, A:D.159, H2O.1 TL.9: 4 residues within 4Å: Chain B: E.73, T.129, S.155, D.159 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.73, B:T.129, B:S.155, B:D.159, H2O.1

1 x UND: UNDECANE(Non-covalent)

UND.7: 4 residues within 4Å: Chain B: W.319, S.320, L.322, G.323 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.322, B:L.322

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

ACT.8: 4 residues within 4Å: Chain B: I.69, E.73, D.130, V.364 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.69 Hydrogen bonds: B:E.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wohlert, D. et al., Structure and substrate ion binding in the sodium/proton antiporter PaNhaP. Elife (2014)

Release Date

2014-12-17

Peptides

NA+/H+ ANTIPORTER, PUTATIVE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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NA+/H+ ANTIPORTER, PUTATIVE