SMTL ID : 9r1e.1

Cryo-EM structure of human MATE1 in complex with MPP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x WRF: 1-methyl-4-phenylpyridin-1-ium(Non-covalent)

WRF.1: 6 residues within 4Å: Chain A: N.82, W.274, Y.277, Y.299, I.303, Y.306 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.303, A:I.303 pi-Stacking: A:W.274, A:W.274, A:Y.306

9 x CLR: CHOLESTEROL(Non-covalent)(Covalent)

CLR.2: 14 residues within 4Å: Chain A: V.83, T.84, V.88, L.92, L.125, C.126, P.129, L.133, W.256, L.260, W.275, L.549 Ligands: CLR.3, CLR.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.83, A:T.84, A:V.88, A:L.92, A:P.129, A:L.260, A:W.275, A:W.275, A:L.549 CLR.3: 13 residues within 4Å: Chain A: P.129, A.132, L.133, N.136, H.139, I.140, L.143, I.556, V.559, V.563, V.567, I.569 Ligands: CLR.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.129, A:A.132, A:L.133, A:N.136, A:H.139, A:I.140, A:I.140, A:L.143, A:L.143, A:I.556, A:V.559, A:V.567, A:I.569 CLR.4: 2 residues within 4Å: Chain A: L.143, R.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.143 Hydrogen bonds: A:R.145 CLR.5: 6 residues within 4Å: Chain A: W.131, L.135, L.557, I.561, F.565 Ligands: CLR.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.131, A:L.135, A:L.557, A:I.561, A:F.565, A:F.565 CLR.6: 4 residues within 4Å: Chain A: P.163, L.218, L.221 Ligands: CLR.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.163, A:P.163, A:L.218, A:L.221 CLR.7: 6 residues within 4Å: Chain A: W.131, T.159, P.166, Y.225 Ligands: CLR.5, CLR.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.131, A:T.159, A:P.166 CLR.8: 5 residues within 4Å: Chain A: I.58, V.61, F.62, V.192, A.199 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.58, A:I.58, A:V.61, A:F.62, A:V.192, A:A.199 CLR.9: 14 residues within 4Å: Chain A: T.75, L.76, A.79, V.80, V.83, I.140, L.141, F.144, Q.146, E.278, S.281, F.282 Chain B: Y.104 Ligands: CLR.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.75, A:L.76, A:A.79, A:V.80, A:V.83, A:I.140, A:L.141, A:F.144, A:F.144, A:F.144, A:F.282, A:F.282 CLR.10: 6 residues within 4Å: Chain A: V.279, F.282, L.283, I.425, F.429 Chain B: F.108 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.279, A:F.282, A:I.425, A:F.429, B:F.108, B:F.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romane, K. et al., Structural basis of drug recognition by human MATE1 transporter. Nat Commun (2025)

Release Date

2025-11-05

Peptides

Multidrug and toxin extrusion protein 1: A
Heavy chain of Fab: B
Light chain of Fab: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Membrane

We predict this structure to be a membrane protein.
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Multidrug and toxin extrusion protein 1

Heavy chain of Fab

Light chain of Fab

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