SMTL ID : 7v5c.1

Cryo-EM structure of the mouse ABCB9 (ADP.BeF3-bound)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 22 residues within 4Å: Chain A: D.274, Y.509, T.511, R.512, V.517, S.537, G.538, S.539, G.540, K.541, S.542, S.543, Y.552 Chain B: K.372, A.637, Q.638, L.639, S.640, G.641, Q.643 Ligands: BEF.2, MG.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.274, A:T.511, A:R.512, A:K.541, A:S.542, A:S.542, A:S.543, B:G.641, B:Q.643, B:Q.643 pi-Stacking: A:Y.509, A:Y.509 ADP.4: 23 residues within 4Å: Chain A: K.372, L.624, A.637, Q.638, L.639, S.640, G.641, Q.643 Chain B: D.274, Y.509, T.511, R.512, V.517, S.537, G.538, S.539, G.540, K.541, S.542, S.543, Y.552 Ligands: BEF.5, MG.6 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.274, B:T.511, B:R.512, B:K.541, B:S.542, B:S.542, B:S.543, A:Q.638, A:G.641, A:Q.643, A:Q.643

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 11 residues within 4Å: Chain A: S.537, K.541, S.542, Q.583, E.664, H.695 Chain B: S.640, G.641, G.642 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 11 residues within 4Å: Chain A: S.640, G.641, G.642 Chain B: S.537, K.541, S.542, Q.583, E.664, H.695 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.542, Q.583, D.663 Ligands: ADP.1, BEF.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.542 MG.6: 5 residues within 4Å: Chain B: S.542, Q.583, D.663 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J.G. et al., The lysosomal transporter TAPL has a dual role as peptide translocator and phosphatidylserine floppase. Nat Commun (2022)

Release Date

2022-10-19

Peptides

ABC-type oligopeptide transporter ABCB9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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ABC-type oligopeptide transporter ABCB9

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