SMTL ID : 7dnz.1

Cryo-EM structure of the human ABCB6 (Hemin and GSH-bound)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 12 residues within 4Å: Chain A: R.435, R.439, L.494, L.497, N.498, Q.501, N.545, W.546, G.548, T.549, R.552 Ligands: HEM.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.435, A:N.498, A:N.545, A:G.548, A:T.549 Salt bridges: A:R.439, A:R.552 GSH.2: 7 residues within 4Å: Chain A: E.346, G.367, L.370, R.371, D.374 Chain B: R.450, Y.476 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.370, B:R.450 Hydrogen bonds: B:Y.476 Salt bridges: B:R.450 GSH.7: 10 residues within 4Å: Chain B: R.439, L.494, L.497, N.498, Q.501, N.545, G.548, T.549, R.552 Ligands: HEM.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.498, B:Q.501, B:Q.501, B:N.545, B:G.548, B:T.549 Salt bridges: B:R.439, B:R.552 GSH.8: 8 residues within 4Å: Chain A: R.450, A.453, Y.476 Chain B: E.346, L.370, R.371, A.373, D.374 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.450, B:L.370 Hydrogen bonds: A:Y.476 Salt bridges: A:R.450

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 4 residues within 4Å: Chain A: N.300, A.303, W.304, T.307 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.303, A:W.304 Y01.4: 7 residues within 4Å: Chain A: W.412, L.415, I.416, L.419, L.507, L.515, E.522 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.412, A:L.415, A:I.416, A:L.419, A:L.507 Y01.5: 4 residues within 4Å: Chain A: M.272, R.276, A.277, I.400 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.276, A:A.277, A:I.400 Y01.9: 3 residues within 4Å: Chain B: M.272, A.277, I.400 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.277, B:I.400 Y01.10: 8 residues within 4Å: Chain B: W.412, L.415, I.416, L.419, L.507, G.508, L.515, E.522 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.412, B:W.412, B:L.415, B:I.416, B:L.419, B:L.507 Y01.11: 3 residues within 4Å: Chain B: A.303, W.304, T.307 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.303, B:W.304

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.6: 8 residues within 4Å: Chain A: W.546, Y.550 Chain B: T.320, Y.386, W.546, Y.550 Ligands: GSH.1, GSH.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:T.320, B:W.546, A:W.546 Hydrogen bonds: A:S.322, A:Y.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., Structural Insights into Porphyrin Recognition by the Human ATP-Binding Cassette Transporter ABCB6. Mol.Cells (2022)

Release Date

2022-06-22

Peptides

ATP-binding cassette sub-family B member 6, mitochondrial: 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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ATP-binding cassette sub-family B member 6, mitochondrial

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