SMTL ID : 7b4l.1

CryoEM structure of the human sodium proton exchanger NHA2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: V.244, P.246, G.275, D.278, D.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.278 NA.13: 5 residues within 4Å: Chain B: V.244, P.246, G.275, D.278, D.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.278

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.2: 18 residues within 4Å: Chain A: D.333, K.334, L.335, V.336, C.337, T.340, F.341, L.344, V.348, I.388 Chain B: V.100, V.391 Ligands: C14.3, UND.6, POV.11, POV.12, C14.15, C14.16 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.341, A:L.344, A:V.348, B:V.100, B:V.391 Salt bridges: A:K.334 POV.11: 20 residues within 4Å: Chain A: L.97, V.101, I.104, T.105, S.107, E.108 Chain B: I.118, I.119, F.122, K.171, W.172, S.175, L.176, I.179, L.399 Ligands: POV.2, POV.12, POV.14, C14.16, UND.18 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.118, B:I.119, B:F.122, B:W.172, B:W.172, B:L.176, B:I.179, B:L.399, A:L.97, A:V.101 Hydrogen bonds: B:S.175 Salt bridges: B:K.171, B:K.171 POV.12: 20 residues within 4Å: Chain A: I.118, I.119, F.122, K.171, W.172, S.175, L.176, I.179, L.399 Chain B: L.97, V.101, I.104, T.105, S.107, E.108 Ligands: POV.2, C14.4, UND.6, POV.11, POV.14 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.118, A:I.119, A:F.122, A:W.172, A:W.172, A:L.176, A:I.179, A:L.399, B:L.97, B:V.101 Hydrogen bonds: A:S.175 Salt bridges: A:K.171, A:K.171 POV.14: 18 residues within 4Å: Chain A: V.100, V.391 Chain B: D.333, K.334, L.335, V.336, C.337, T.340, F.341, L.344, V.348, I.388 Ligands: C14.3, C14.4, POV.11, POV.12, C14.15, UND.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.341, B:L.344, B:V.348, A:V.100, A:V.391 Salt bridges: B:K.334

6 x C14: TETRADECANE(Non-covalent)

C14.3: 6 residues within 4Å: Chain A: I.179, I.388, V.391, F.396 Ligands: POV.2, POV.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.179, A:I.388, A:V.391, A:F.396 C14.4: 9 residues within 4Å: Chain A: L.97, F.122, I.126, K.130, D.394, I.395 Ligands: POV.12, POV.14, UND.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.97, A:F.122, A:F.122, A:I.126, A:I.395 C14.5: 3 residues within 4Å: Chain A: W.98, W.102 Chain B: L.349 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.98, A:W.102, A:W.102, A:W.102, B:L.349 C14.15: 6 residues within 4Å: Chain B: I.179, I.388, V.391, F.396 Ligands: POV.2, POV.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.179, B:I.388, B:V.391, B:F.396 C14.16: 9 residues within 4Å: Chain B: L.97, F.122, I.126, K.130, D.394, I.395 Ligands: POV.2, UND.6, POV.11 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.97, B:F.122, B:F.122, B:I.126, B:I.395 C14.17: 3 residues within 4Å: Chain A: L.349 Chain B: W.98, W.102 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.98, B:W.102, B:W.102, B:W.102, A:L.349

10 x UND: UNDECANE(Non-covalent)

UND.6: 7 residues within 4Å: Chain A: K.334, C.337, K.338, F.341 Ligands: POV.2, POV.12, C14.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.334, A:K.338, A:F.341 UND.7: 5 residues within 4Å: Chain A: I.94, W.98, P.111, F.116, I.120 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.94, A:W.98, A:W.98, A:F.116, A:I.120 UND.8: 1 residues within 4Å: Chain A: R.86 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.86 UND.9: 2 residues within 4Å: Chain A: F.357, F.359 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.357, A:F.357, A:F.359 UND.10: 4 residues within 4Å: Chain A: Q.232, F.235, T.288, C.289 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.235, A:T.288 UND.18: 7 residues within 4Å: Chain B: K.334, C.337, K.338, F.341 Ligands: C14.4, POV.11, POV.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.334, B:K.338, B:F.341 UND.19: 5 residues within 4Å: Chain B: I.94, W.98, P.111, F.116, I.120 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.94, B:W.98, B:W.98, B:F.116, B:I.120 UND.20: 1 residues within 4Å: Chain B: R.86 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.86 UND.21: 2 residues within 4Å: Chain B: F.357, F.359 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.357, B:F.357, B:F.359 UND.22: 4 residues within 4Å: Chain B: Q.232, F.235, T.288, C.289 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.235, B:T.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woehlert, D. et al., CryoEM structure of the human sodium proton exchanger NHA2. To Be Published

Release Date

2022-01-12

Peptides

Sodium/hydrogen exchanger 9B2: 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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Sodium/hydrogen exchanger 9B2

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