SMTL ID : 7x0z.1

Cryo-EM structure of human ABCD1 E630Q in the presence of ATP and Magnesium in outward-facing state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.532, Q.562, D.647, Q.648 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.532, A:D.647 MG.3: 3 residues within 4Å: Chain B: S.532, Q.562 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.532

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 25 residues within 4Å: Chain A: R.454, T.501, P.502, P.526, N.527, G.528, C.529, G.530, K.531, S.532, S.533, R.536, W.542, Q.562, Q.648, H.677 Chain B: R.609, D.621, V.622, S.624, G.625, G.626, E.627, A.652 Ligands: MG.1 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:R.609, B:R.609, B:D.621, B:G.625, B:G.626, B:E.627, B:A.652, A:R.454, A:N.527, A:C.529, A:G.530, A:K.531, A:S.532, A:S.533, A:R.536, A:Q.562, A:Q.648 Salt bridges: A:K.531, A:K.531 ATP.4: 23 residues within 4Å: Chain A: R.609, D.621, V.622, L.623, S.624, G.625, G.626, E.627 Chain B: T.501, P.502, P.526, N.527, G.528, C.529, G.530, K.531, S.532, S.533, R.536, W.542, Q.562, Q.648 Ligands: MG.3 21 PLIP interactions: 13 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:P.526, B:N.527, B:G.528, B:G.528, B:C.529, B:G.530, B:K.531, B:S.532, B:S.533, B:Q.648, A:R.609, A:R.609, A:D.621, A:S.624, A:S.624, A:G.625, A:G.626, A:E.627 Salt bridges: B:K.531, B:K.531, B:R.536

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiong, C. et al., Structural insights into substrate recognition and translocation of human peroxisomal ABC transporter ALDP. Signal Transduct Target Ther (2023)

Release Date

2023-03-22

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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