SMTL ID : 7lkz.1

Structure of ATP-bound 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: 4 residues within 4Å: Chain A: N.415, E.419, L.522, D.523 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.523

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: 5 residues within 4Å: Chain A: P.85, Q.1481, V.1482, N.1529, D.1532 No protein-ligand interaction detected (PLIP)

3 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.3: 13 residues within 4Å: Chain A: R.653, I.777, L.778, F.780, A.781, Q.783, L.1390, S.1391, I.1394, E.1670, L.1674, S.1677, V.1678 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.777, A:L.778, A:I.1394, A:L.1674 Hydrogen bonds: A:R.653 Salt bridges: A:R.653 6OU.4: 5 residues within 4Å: Chain A: F.754, F.755, S.756, L.760, K.1371 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.754, A:F.754 Hydrogen bonds: A:F.754, A:S.756 6OU.5: 9 residues within 4Å: Chain A: Q.21, I.23, R.24, Y.665, L.1784, F.1785, D.1786, V.1787, A.1794 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.23, A:F.1785, A:A.1794 Hydrogen bonds: A:Q.21, A:Y.665, A:D.1786, A:V.1787

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

POV.6: 3 residues within 4Å: Chain A: Y.516, L.517 Ligands: POV.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.516, A:L.517 POV.7: 3 residues within 4Å: Chain A: L.382, A.386, W.387 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.386, A:W.387 POV.8: 7 residues within 4Å: Chain A: I.73, L.393, F.418, L.421, L.522, K.524 Ligands: POV.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.73, A:L.393, A:F.418, A:L.421, A:L.522 POV.9: 7 residues within 4Å: Chain A: F.74, V.77, N.78, M.316, L.323 Ligands: POV.6, POV.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.74, A:V.77, A:L.323 POV.10: 6 residues within 4Å: Chain A: Q.71, S.95, Y.97, L.1566, P.1567, V.1568 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.1567, A:P.1567

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

NAG.11: 1 residues within 4Å: Chain A: N.444 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.504 NAG.13: 2 residues within 4Å: Chain A: N.1469, Q.1472 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: Y.440, N.1588 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1588 NAG.15: 3 residues within 4Å: Chain A: T.532, E.1399, N.1662 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain A: N.98, R.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.107, A:R.107

2 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 3 residues within 4Å: Chain A: T.1979, Q.2019 Ligands: ATP.20 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: T.970, Q.1010 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.970

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

ATP.19: 15 residues within 4Å: Chain A: F.938, A.945, N.965, G.966, G.968, K.969, T.970, T.971, Q.1010, H.1118, T.2070, S.2072, G.2073, G.2074 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.965, A:G.966, A:G.966, A:A.967, A:G.968, A:K.969, A:T.970, A:T.971, A:G.2073, A:G.2074 Salt bridges: A:K.969, A:K.969, A:H.1118 pi-Stacking: A:F.938, A:F.938 ATP.20: 17 residues within 4Å: Chain A: K.1054, E.1057, D.1061, S.1063, G.1064, G.1065, Y.1947, N.1974, G.1975, G.1977, K.1978, T.1979, T.1980, Q.2019, Q.2096, H.2128 Ligands: MG.17 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.1054, A:K.1054, A:E.1057, A:S.1063, A:G.1064, A:G.1065, A:G.1975, A:G.1975, A:G.1977, A:K.1978, A:T.1979, A:T.1980, A:Q.2019, A:Q.2096 Salt bridges: A:K.1978, A:K.1978, A:H.2128 pi-Stacking: A:Y.1947, A:Y.1947

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