SMTL ID : 7p1k.1

Cryo EM structure of bison NHA2 in nano disc structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

8 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 11 residues within 4Å: Chain A: W.230, Q.231, F.234, F.238, L.280, T.283, G.284, M.291, V.302, G.305, V.306 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.234, A:L.280, A:T.283 Y01.4: 10 residues within 4Å: Chain A: I.94, L.95, W.97, A.98, W.101, L.109 Chain B: L.348, S.352, F.356 Ligands: Y01.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.348, B:F.356, A:W.101 Y01.5: 10 residues within 4Å: Chain A: V.93, I.94, W.97, P.110, F.115, M.119, Y.122, I.126 Ligands: Y01.4, Y01.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.94, A:W.97, A:W.97 Y01.6: 8 residues within 4Å: Chain A: P.110, F.115, M.119, C.123, I.126, I.161, N.164 Ligands: Y01.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.110, A:F.115, A:I.161 Y01.7: 10 residues within 4Å: Chain A: L.345, L.348, S.352, F.356 Chain B: I.94, L.95, W.97, A.98, W.101 Ligands: Y01.8 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.348, A:F.356, B:I.94, B:W.101, B:W.101 Hydrogen bonds: A:Y.355 Y01.8: 10 residues within 4Å: Chain B: V.93, I.94, W.97, P.110, F.115, M.119, Y.122, I.126 Ligands: Y01.7, Y01.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.94, B:W.97, B:I.126 Y01.9: 8 residues within 4Å: Chain B: P.110, F.115, M.119, C.123, I.126, I.161, N.164 Ligands: Y01.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.110, B:F.115, B:I.126 Y01.10: 12 residues within 4Å: Chain B: W.230, Q.231, F.234, F.238, L.280, T.283, G.284, T.287, M.291, V.302, G.305, V.306 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.234, B:L.280, B:T.283

4 x T7X: Phosphatidylinositol(Non-covalent)

T7X.2: 4 residues within 4Å: Chain A: W.336, V.387, V.390, A.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.387 T7X.3: 15 residues within 4Å: Chain A: V.100, L.114, K.170, W.171, A.174, L.175, V.347, F.395 Chain B: V.99, V.100, V.103, T.104, E.107, L.114 Ligands: T7X.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.99, B:V.103, B:L.114 Hydrogen bonds: A:K.170 T7X.11: 5 residues within 4Å: Chain B: W.336, V.387, V.390, A.391 Ligands: T7X.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.387 T7X.12: 17 residues within 4Å: Chain A: V.99, V.100, V.103, T.104, L.114 Chain B: V.100, L.114, I.118, K.170, W.171, A.174, L.175, I.178, V.347, F.395 Ligands: T7X.3, T7X.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.99, A:V.103, A:L.114 Hydrogen bonds: B:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuoka, R. et al., Structure, mechanism and lipid-mediated remodeling of the mammalian Na + /H + exchanger NHA2. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-01-26

Peptides

mitochondrial sodium/hydrogen exchanger 9B2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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mitochondrial sodium/hydrogen exchanger 9B2

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