SMTL ID : 9r10.1

Cryo-EM structure of human MATE1 in complex with cimetidine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

9 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 13 residues within 4Å: Chain A: T.75, L.76, A.79, V.83, F.144, Q.146, E.278, V.279, S.281, F.282 Chain B: Y.104 Ligands: CLR.2, CLR.10 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.104, A:T.75, A:L.76, A:A.79, A:V.83, A:F.144, A:V.279, A:F.282, A:F.282 CLR.2: 12 residues within 4Å: Chain A: V.83, T.84, V.88, L.92, L.125, C.126, L.133, M.267, W.275, L.549 Ligands: CLR.1, CLR.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.83, A:T.84, A:V.88, A:V.88, A:L.92, A:W.275, A:L.549 CLR.3: 9 residues within 4Å: Chain A: L.133, N.136, H.139, I.140, L.143, I.556, V.559, V.563 Ligands: CLR.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: 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 CLR.4: 3 residues within 4Å: Chain A: L.143, R.145 Chain B: F.108 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.143, B:F.108 Hydrogen bonds: A:R.145 CLR.5: 6 residues within 4Å: Chain A: F.128, W.131, L.135, T.159, I.561, F.565 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.128, A:T.159, A:I.561, A:F.565 CLR.6: 4 residues within 4Å: Chain A: P.163, L.218, L.221, Y.225 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.163, A:L.218, A:L.221 CLR.7: 8 residues within 4Å: Chain A: L.50, M.51, L.54, I.58, F.62, L.196, A.199 Ligands: CLR.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.50, A:I.58, A:I.58, A:L.196 CLR.9: 5 residues within 4Å: Chain A: L.196, A.199, L.200, Y.203 Ligands: CLR.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.196, A:L.200, A:Y.203, A:Y.203 CLR.10: 8 residues within 4Å: Chain A: V.279, F.282, L.283, I.286, I.425, F.429 Chain B: F.108 Ligands: CLR.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.279, A:F.282, A:L.283, A:I.286, A:I.425, A:F.429, A:F.429, B:F.108, B:F.108

1 x SD9: Cimetidine(Non-covalent)

SD9.8: 8 residues within 4Å: Chain A: N.82, W.274, Y.277, Y.299, A.302, I.303, Y.306, E.389 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.306 Hydrogen bonds: A:Y.299, A:E.389, A:E.389

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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