SMTL ID : 8eop.1

Cryo-EM Structure of Nanodisc reconstituted human ABCA7 EQ mutant in ATP bound closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: F.1283, F.1318, N.1381 No protein-ligand interaction detected (PLIP)

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: 7 residues within 4Å: Chain A: P.83, Q.84, L.85, E.1339, S.1340, N.1386, D.1389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.84

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

NAG.3: 2 residues within 4Å: Chain A: N.78, L.279 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.98, D.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.99, A:D.99 NAG.5: 3 residues within 4Å: Chain A: N.312, L.409, D.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.410 NAG.6: 2 residues within 4Å: Chain A: N.340, D.341 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: H.1265, N.1518 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.1265 NAG.8: 4 residues within 4Å: Chain A: D.323, R.1453, K.1456, N.1457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.323, A:N.1457

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

ATP.9: 20 residues within 4Å: Chain A: K.932, R.938, H.939, S.941, G.942, G.943, M.944, Y.1802, A.1809, V.1828, N.1829, G.1830, A.1831, G.1832, K.1833, T.1834, S.1835, Q.1874, Q.1951 Ligands: MG.11 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.932, A:K.932, A:H.939, A:S.941, A:G.942, A:G.943, A:V.1828, A:N.1829, A:G.1830, A:G.1830, A:A.1831, A:G.1832, A:K.1833, A:T.1834, A:S.1835, A:Q.1874, A:Q.1951 Salt bridges: A:K.1833, A:K.1833 pi-Stacking: A:Y.1802, A:Y.1802 ATP.12: 15 residues within 4Å: Chain A: F.816, S.819, A.823, N.843, G.844, G.846, K.847, T.848, T.849, H.996, Y.1918, T.1925, S.1927, G.1928 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.819, A:N.843, A:G.844, A:G.846, A:K.847, A:T.848, A:T.848, A:T.848, A:T.849, A:Y.1918, A:T.1925, A:S.1927, A:G.1928 Salt bridges: A:K.847, A:K.847, A:H.996 pi-Stacking: A:F.816

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain A: T.848, Q.888, S.1927 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: T.1834, Q.1874, Q.1951 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1834

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Le, L.T.M. et al., Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. Embo J. (2023)

Release Date

2022-12-21

Peptides

Phospholipid-transporting ATPase ABCA7: 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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Phospholipid-transporting ATPase ABCA7