SMTL ID : 7vzb.1

Cryo-EM structure of C22:0-CoA bound human very long-chain fatty acid ABC transporter ABCD1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 7 residues within 4Å: Chain A: S.270, L.274, G.292, V.295, F.296, I.443 Ligands: FFI.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.274, A:V.295, A:F.296 Y01.3: 5 residues within 4Å: Chain B: V.266, S.270, V.295, I.443 Ligands: FFI.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.266, B:V.295, B:I.443

2 x FFI: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] docosanethioate(Non-covalent)

FFI.2: 25 residues within 4Å: Chain A: R.280, V.295, Q.376, K.380, Y.381, W.383, G.387, M.390, P.394, I.395, A.428, A.432, L.436, A.439, A.440 Chain B: R.148, W.181, A.188, N.192, I.195, R.196, S.257, K.261, R.445 Ligands: Y01.1 21 PLIP interactions: 9 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:W.181, A:R.280, A:V.295, A:I.395, A:A.428, A:A.432, A:A.439 Hydrogen bonds: B:N.192, B:S.257, B:S.257, B:R.445, A:Q.376, A:K.380, A:Y.381 Salt bridges: B:R.148, B:R.148, B:R.196, A:K.380, A:K.380, A:K.380 pi-Cation interactions: B:R.445 FFI.4: 25 residues within 4Å: Chain A: R.148, W.181, A.188, N.192, I.195, R.196, S.257, K.261, R.445 Chain B: R.280, V.295, Q.376, K.380, Y.381, W.383, G.387, M.390, P.394, I.395, A.428, A.432, L.436, A.439, A.440 Ligands: Y01.3 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:R.280, B:V.295, B:I.395, B:A.428, B:A.432, B:A.439, A:W.181 Hydrogen bonds: B:Q.376, B:K.380, B:Y.381, A:N.192, A:S.257, A:S.257 Salt bridges: B:K.380, B:K.380, B:K.380, A:R.148, A:R.148, A:R.196 pi-Cation interactions: A:R.445, A:R.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z.P. et al., Structural basis of substrate recognition and translocation by human very long-chain fatty acid transporter ABCD1. Nat Commun (2022)

Release Date

2022-05-18

Peptides

Peroxisomal Membrane Protein related,ATP-binding cassette sub-family D member 1: 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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Peroxisomal Membrane Protein related,ATP-binding cassette sub-family D member 1

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