SMTL ID : 9r1f.1

Cryo-EM structure of human MATE1 in complex with metformin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 11 residues within 4Å: Chain A: V.88, L.125, C.126, P.129, L.133, L.260, I.264, M.267, W.275, L.549 Ligands: CLR.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.88, A:L.125, A:P.129, A:P.129, A:I.264, A:W.275 CLR.2: 7 residues within 4Å: Chain A: F.144, L.283, I.286, I.425 Chain B: F.108, W.109 Chain C: S.50 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.144, A:L.283, A:I.286, A:I.425, B:W.109 Hydrogen bonds: C:S.50, C:S.50 CLR.3: 6 residues within 4Å: Chain A: W.131, L.135, T.159, I.561, R.564, F.565 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.159, A:I.561, A:F.565, A:F.565 CLR.4: 4 residues within 4Å: Chain A: L.196, A.199, L.200, Y.203 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.196, A:L.196, A:Y.203, A:Y.203, A:Y.203 CLR.5: 13 residues within 4Å: Chain A: T.75, L.76, A.79, V.83, I.140, F.144, Q.146, E.278, S.281, F.282, L.292 Chain B: Y.104 Ligands: CLR.1 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.75, A:L.76, A:A.79, A:V.83, A:I.140, A:I.140, A:F.144, A:F.144, A:F.282, A:F.282, B:Y.104

1 x MF8: Metformin(Non-covalent)

MF8.6: 6 residues within 4Å: Chain A: E.273, Y.277, Y.299, A.302, Y.306, E.389 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.277, A:Y.277 Water bridges: A:A.302, A:E.389 Salt bridges: A:E.273, A:E.389, A:E.389 pi-Cation interactions: A:Y.277, A:Y.306

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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