SMTL ID : 9dbq.1

Cryo-EM structure of human ABCB6 transporter in an inward-facing conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

20 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)(Covalent)

Y01.1: 5 residues within 4Å: Chain A: A.303, W.304, T.307 Chain B: L.510 Ligands: Y01.5 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.510, A:W.304, A:W.304, A:T.307 Y01.2: 5 residues within 4Å: Chain A: G.273, A.277, V.280, L.281, F.408 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.277, A:L.281, A:F.408 Y01.3: 9 residues within 4Å: Chain A: W.412, L.419, L.507, G.508, A.511, L.515, K.524 Ligands: Y01.4, Y01.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.412, A:W.412, A:W.412, A:L.419, A:A.511, A:L.515 Salt bridges: A:K.524 Y01.4: 6 residues within 4Å: Chain A: I.402, A.411, W.412, L.415, F.418 Ligands: Y01.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.402, A:A.411, A:A.411, A:W.412, A:W.412, A:W.412, A:L.415, A:F.418, A:F.418, A:F.418 Y01.5: 4 residues within 4Å: Chain A: F.285, W.304, S.308 Ligands: Y01.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.285, A:W.304, A:W.304 Y01.6: 7 residues within 4Å: Chain A: N.390, T.394, P.543, L.544, W.546, F.547, Y.550 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.394, A:W.546, A:W.546, A:F.547, A:F.547, A:F.547, A:Y.550 Hydrogen bonds: A:Y.550 Y01.7: 10 residues within 4Å: Chain A: W.434, K.437, F.438, K.489, A.492, S.493, V.495, L.496, Q.499 Chain B: F.325 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.434, A:W.434, A:F.438, A:F.438, A:A.492, A:V.495, A:L.496, A:Q.499 Salt bridges: A:K.437, A:K.489 Y01.8: 5 residues within 4Å: Chain A: V.431, W.434, T.500, L.503, L.507 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.431, A:T.500, A:L.503, A:L.507 Salt bridges: A:K.437 Y01.9: 6 residues within 4Å: Chain A: L.507, A.511, L.514, Y.518 Chain B: W.299 Ligands: Y01.3 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.299, A:L.507, A:L.514, A:Y.518, A:Y.518 Y01.10: 7 residues within 4Å: Chain A: S.258, A.260, L.261, V.264, I.267, F.325, R.336 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.260, A:L.261, A:V.264, A:I.267, A:F.325 Hydrogen bonds: A:S.258 Salt bridges: A:R.336 Y01.11: 6 residues within 4Å: Chain A: W.299 Chain B: L.507, A.511, L.514, Y.518 Ligands: Y01.15 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.299, B:L.507, B:L.514, B:Y.518, B:Y.518 Y01.12: 7 residues within 4Å: Chain B: S.258, A.260, L.261, V.264, I.267, F.325, R.336 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.260, B:L.261, B:V.264, B:I.267, B:F.325 Hydrogen bonds: B:S.258 Salt bridges: B:R.336 Y01.13: 5 residues within 4Å: Chain A: L.510 Chain B: A.303, W.304, T.307 Ligands: Y01.17 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.304, B:W.304, B:T.307, A:L.510 Y01.14: 5 residues within 4Å: Chain B: G.273, A.277, V.280, L.281, F.408 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.277, B:L.281, B:F.408 Y01.15: 9 residues within 4Å: Chain B: W.412, L.419, L.507, G.508, A.511, L.515, K.524 Ligands: Y01.11, Y01.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.412, B:W.412, B:W.412, B:L.419, B:A.511, B:L.515 Salt bridges: B:K.524 Y01.16: 6 residues within 4Å: Chain B: I.402, A.411, W.412, L.415, F.418 Ligands: Y01.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.402, B:A.411, B:A.411, B:W.412, B:W.412, B:L.415, B:F.418, B:F.418, B:F.418 Y01.17: 4 residues within 4Å: Chain B: F.285, W.304, S.308 Ligands: Y01.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.285, B:W.304, B:W.304 Y01.18: 7 residues within 4Å: Chain B: N.390, T.394, P.543, L.544, W.546, F.547, Y.550 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.394, B:W.546, B:W.546, B:F.547, B:F.547, B:F.547, B:Y.550 Hydrogen bonds: B:Y.550 Y01.19: 10 residues within 4Å: Chain A: F.325 Chain B: W.434, K.437, F.438, K.489, A.492, S.493, V.495, L.496, Q.499 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.434, B:W.434, B:A.492, B:V.495, B:L.496, B:Q.499 Salt bridges: B:K.437, B:K.489 Y01.20: 5 residues within 4Å: Chain B: V.431, W.434, T.500, L.503, L.507 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.431, B:T.500, B:L.503, B:L.507 Salt bridges: B:K.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baril, S.A. et al., The role of ATP-binding Cassette subfamily B member 6 in the inner ear. Nat Commun (2024)

Release Date

2024-11-20

Peptides

ATP-binding cassette sub-family B member 6: 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

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