SMTL ID : 9quw.1

Cryo-EM structure of the human NHA2-Fab complex bound to phloretin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x LPP: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE(Non-covalent)

LPP.1: 21 residues within 4Å: Chain D: K.169, K.171, W.172, S.175, L.176, I.179, I.183, F.341, L.344, G.345, V.348, A.392, F.396 Chain E: V.100, V.101, I.104, T.105, E.108, L.115, W.172 Ligands: LPP.3 11 PLIP interactions: 3 interactions with chain E, 8 interactions with chain D Hydrophobic interactions: E:V.100, E:I.104, E:I.104, D:W.172, D:W.172, D:W.172, D:F.341, D:F.396 Hydrogen bonds: D:W.172 Salt bridges: D:K.169, D:K.171 LPP.3: 21 residues within 4Å: Chain D: V.100, V.101, I.104, T.105, E.108, L.115, W.172 Chain E: K.169, K.171, W.172, S.175, L.176, I.179, I.183, F.341, L.344, G.345, V.348, A.392, F.396 Ligands: LPP.1 11 PLIP interactions: 3 interactions with chain D, 8 interactions with chain E Hydrophobic interactions: D:V.100, D:I.104, D:I.104, E:W.172, E:W.172, E:W.172, E:F.341, E:F.396 Hydrogen bonds: E:W.172 Salt bridges: E:K.169, E:K.171

2 x G50: 3-(4-HYDROXYPHENYL)-1-(2,4,6-TRIHYDROXYPHENYL)PROPAN-1-ONE(Non-covalent)

G50.2: 15 residues within 4Å: Chain D: L.181, L.185, P.246, D.279, I.283, F.286, N.287, P.360, G.361, G.364, T.462, V.463, A.466, I.467, V.470 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.181, D:I.283, D:P.360, D:A.466, D:I.467 Hydrogen bonds: D:D.279, D:T.462 G50.4: 15 residues within 4Å: Chain E: L.181, L.185, P.246, D.279, I.283, F.286, N.287, P.360, G.361, G.364, T.462, V.463, A.466, I.467, V.470 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.181, E:I.283, E:P.360, E:A.466, E:I.467 Hydrogen bonds: E:D.279, E:T.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, S. et al., Structure and Inhibition of the Human Na + /H + Exchanger SLC9B2. Int J Mol Sci (2025)

Release Date

2025-05-14

Peptides

Fab light chain: AF
Fab heavy chain: BC
Sodium/hydrogen exchanger 9B2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

F
C

B
D

C
F

D
A

E
B

Membrane

We predict this structure to be a membrane protein.
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Fab light chain

Fab heavy chain

Sodium/hydrogen exchanger 9B2

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