SMTL ID : 7rr9.1

Cryo-EM Structure of Nanodisc reconstituted ABCD1 in nucleotide bound outward open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x UNL: UNKNOWN LIGAND

UNL.1: 4 residues within 4Å: Chain A: F.71, L.72, L.211, Y.212 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.71, A:L.72, A:L.211, A:Y.212 UNL.7: 6 residues within 4Å: Chain B: M.67, L.72, L.75, L.211, Y.212, R.259 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.67, B:L.72, B:L.75, B:L.211, B:Y.212

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 5 residues within 4Å: Chain A: L.79, R.80, F.83, T.91, L.94 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.83, A:L.94 CLR.8: 5 residues within 4Å: Chain B: L.79, R.80, F.83, T.91, L.94 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.83, B:T.91, B:L.94

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.514, Q.544 Chain B: G.607 Ligands: AGS.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: S.514, Q.544 Ligands: AGS.6 No protein-ligand interaction detected (PLIP)

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.4: 15 residues within 4Å: Chain A: P.508, N.509, G.512, K.513, S.514, S.515, R.518, Q.544, E.630 Chain B: R.591, D.603, V.604, S.606, G.608 Ligands: MG.3 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.513, A:K.513, A:S.514, A:S.515, B:S.606, B:G.608 Salt bridges: A:R.518 AGS.6: 16 residues within 4Å: Chain A: R.591, V.604, S.606, G.607, G.608 Chain B: P.508, N.509, G.512, K.513, S.514, S.515, R.518, W.524, Q.544, E.630 Ligands: MG.5 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.509, B:G.512, B:K.513, B:K.513, B:S.514, B:S.515, A:S.606, A:S.606, A:S.606, A:G.608 Salt bridges: B:R.518

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le, L.T.M. et al., Structures of the human peroxisomal fatty acid transporter ABCD1 in a lipid environment. Commun Biol (2022)

Release Date

2022-01-19

Peptides

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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ATP-binding cassette sub-family D member 1

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