SMTL ID : 7m1q.1

Human ABCA4 structure in complex with N-ret-PE

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: S.84, P.85, S.90, Q.1481, V.1482, P.1484, N.1529, D.1532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.84, A:V.1482

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: K.412, N.415, E.422, R.425, L.522, D.523 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.523 Hydrogen bonds: A:R.425

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.98, R.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.107 NAG.4: 3 residues within 4Å: Chain A: Q.437, Y.440, N.1588 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.440 NAG.5: 2 residues within 4Å: Chain A: T.535, N.1662 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.444 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.1469 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1469 NAG.9: 4 residues within 4Å: Chain A: W.439, M.494, R.500, N.504 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.439

1 x HZL: [(2S)-3-[2-[(E)-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenylidene]amino]ethoxy-oxidanyl-phosphoryl]oxy-2-[(Z)-octadec-9-enoyl]oxy-propyl] (Z)-octadec-9-enoate(Non-covalent)

HZL.6: 13 residues within 4Å: Chain A: L.42, N.46, Y.340, Y.345, R.587, Y.588, I.649, R.653, F.1397, F.1550, L.1674, S.1677, L.1815 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.42, A:Y.340, A:Y.340, A:Y.345, A:Y.345, A:I.649, A:F.1397, A:F.1397, A:L.1674, A:L.1815 Hydrogen bonds: A:R.587 Salt bridges: A:R.587, A:R.653

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain A: S.336, N.338, D.600 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scortecci, J.F. et al., Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nat Commun (2021)

Release Date

2021-09-08

Peptides

Retinal-specific phospholipid-transporting ATPase ABCA4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Retinal-specific phospholipid-transporting ATPase ABCA4

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