SMTL ID : 7lkp.1

Structure of ATP-free human ABCA4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: L.411, N.415, E.419, E.422, R.425, L.522, D.523 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.422

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.2: 7 residues within 4Å: Chain A: P.85, P.91, Q.1481, V.1482, P.1484, N.1529, D.1532 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.444 NAG.4: 3 residues within 4Å: Chain A: R.500, D.501, N.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.500 NAG.5: 1 residues within 4Å: Chain A: N.1469 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: Y.440, N.1588 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: T.532, T.535, E.1399, N.1662 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.1399 Hydrogen bonds: A:T.532 NAG.8: 3 residues within 4Å: Chain A: I.93, N.98, R.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.98, A:R.107, A:R.107

7 x CLR: CHOLESTEROL(Non-covalent)

CLR.9: 12 residues within 4Å: Chain A: L.760, A.763, V.767, K.1371, L.1699, P.1788, S.1789, Y.1792, V.1793, S.1796, C.1797 Ligands: POV.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.760, A:V.767, A:L.1699, A:P.1788, A:Y.1792, A:V.1793 Hydrogen bonds: A:K.1371 CLR.11: 5 residues within 4Å: Chain A: L.11, W.12, W.15, L.702, S.706 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.15, A:W.15 CLR.13: 5 residues within 4Å: Chain A: V.1360, F.1363, W.1730, M.1733 Ligands: CLR.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1360, A:F.1363, A:F.1363 CLR.14: 9 residues within 4Å: Chain A: T.1366, I.1367, S.1369, H.1370, F.1373, W.1730, M.1733, N.1734 Ligands: CLR.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1373, A:F.1373, A:W.1730, A:W.1730, A:M.1733 CLR.15: 6 residues within 4Å: Chain A: P.1780, F.1783, L.1784, L.1892, V.1896, F.1900 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.1780, A:L.1784, A:L.1784, A:L.1892, A:V.1896 CLR.16: 5 residues within 4Å: Chain A: I.23, W.31, I.664 Ligands: AJP.12, CLR.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.23, A:W.31, A:I.664 CLR.17: 5 residues within 4Å: Chain A: T.1790, V.1793, C.1797 Ligands: AJP.12, CLR.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.1790, A:V.1793

7 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)(Covalent)

POV.10: 4 residues within 4Å: Chain A: F.755, S.756, L.760 Ligands: POV.23 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.760 POV.18: 3 residues within 4Å: Chain A: F.312, T.383, A.386 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.312, A:F.312, A:A.386 POV.19: 5 residues within 4Å: Chain A: I.73, L.393, L.394, F.418, L.421 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.73, A:L.393, A:L.394, A:F.418, A:L.421 POV.20: 3 residues within 4Å: Chain A: F.74 Ligands: POV.21, POV.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.74 POV.21: 2 residues within 4Å: Chain A: Q.71 Ligands: POV.20 No protein-ligand interaction detected (PLIP) POV.22: 3 residues within 4Å: Chain A: Y.516, L.517 Ligands: POV.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.516, A:L.517 POV.23: 5 residues within 4Å: Chain A: C.764, T.771, K.1371 Ligands: CLR.9, POV.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.1371

1 x AJP: Digitonin(Non-covalent)

AJP.12: 17 residues within 4Å: Chain A: I.664, Y.665, S.668, M.669, K.672, L.676, E.679, L.680, A.758, S.759, A.762, H.1016, Q.1060, T.1790, V.1793 Ligands: CLR.16, CLR.17 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.664, A:Y.665, A:K.672, A:A.762 Hydrogen bonds: A:K.672, A:K.672, A:S.759, A:Q.1060 Salt bridges: A:K.672, A:H.1016, A:H.1016

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., Molecular structures of the eukaryotic retinal importer ABCA4. Elife (2021)

Release Date

2021-03-03

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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