SMTL ID : 7vx8.1

Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: T.527, P.528, S.529, P.552, N.553, G.554, C.555, G.556, K.557, S.558, S.559, R.562, W.568, Q.588, Q.674, H.703 Chain B: R.635, V.648, L.649, S.650, G.651, G.652, E.653 Ligands: MG.2 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:R.635, B:R.635, B:D.647, B:S.650, B:S.650, B:G.651, B:G.652, B:E.653, A:T.527, A:P.552, A:N.553, A:G.554, A:G.554, A:C.555, A:G.556, A:K.557, A:S.558, A:S.559, A:R.562, A:Q.588, A:Q.674 Salt bridges: A:K.557, A:K.557, A:R.562 ATP.3: 24 residues within 4Å: Chain A: R.635, V.648, L.649, S.650, G.651, G.652, E.653 Chain B: T.527, P.528, S.529, P.552, N.553, G.554, C.555, G.556, K.557, S.558, S.559, R.562, W.568, Q.588, Q.674, H.703 Ligands: MG.4 26 PLIP interactions: 18 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.527, B:P.552, B:N.553, B:G.554, B:G.554, B:C.555, B:G.556, B:K.557, B:S.558, B:S.559, B:S.559, B:R.562, B:Q.588, B:Q.674, A:R.635, A:R.635, A:D.647, A:S.650, A:S.650, A:G.651, A:G.652, A:E.653 Salt bridges: B:K.557, B:K.557, B:R.562, B:H.703

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.558, Q.588 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.558 MG.4: 3 residues within 4Å: Chain B: S.558, Q.588 Ligands: ATP.3 No protein-ligand interaction detected (PLIP)

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
B

B
A

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