SMTL ID : 7zyi.1

Structure of the human sodium/bile acid cotransporter (NTCP) in complex with Fab and nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 10 residues within 4Å: Chain A: S.206, A.207, V.210, M.215, F.216, A.217, M.218, F.284, L.287, L.288 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.207, A:V.210, A:V.210, A:M.215, A:M.218, A:F.284, A:L.287, A:L.288 CLR.4: 7 residues within 4Å: Chain A: F.231, L.235, Y.238, G.248, R.251, R.252, L.300 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.231, A:L.235, A:Y.238, A:Y.238, A:R.252, A:L.300

2 x CHO: GLYCOCHENODEOXYCHOLIC ACID(Non-covalent)

CHO.2: 9 residues within 4Å: Chain A: L.31, V.202, T.203, Q.264, S.267, L.287, M.290, I.291 Ligands: CHO.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.31, A:L.31, A:V.202, A:T.203, A:L.287, A:M.290 Hydrogen bonds: A:T.203, A:Q.264, A:S.267 CHO.3: 9 residues within 4Å: Chain A: M.34, L.35, I.38, N.103, L.104, N.262, Q.264, M.290 Ligands: CHO.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.38, A:N.103 Hydrogen bonds: A:N.262

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

NA.5: 5 residues within 4Å: Chain A: Q.68, G.97, C.98, S.99, Q.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.261, A:Q.261 NA.6: 5 residues within 4Å: Chain A: S.105, N.106, S.119, T.123, E.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.105, A:N.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Structure of human NTCP reveals the basis of recognition and sodium-driven transport of bile salts into the liver. Cell Res. (2022)

Release Date

2022-07-13

Peptides

Sodium/bile acid cotransporter: A
heavy chain of Fab: B
light chain of Fab: C
Nanobody: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

D
K

Membrane

We predict this structure to be a membrane protein.
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Sodium/bile acid cotransporter

heavy chain of Fab

light chain of Fab

Nanobody

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