SMTL ID : 8edw.1

Cryo-EM Structure of human ABCA7 in BPL/Ch Nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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: 5 residues within 4Å: Chain A: F.1283, H.1313, S.1314, N.1381, T.1383 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.1518, L.1716 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.78, L.282 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.282 NAG.4: 2 residues within 4Å: Chain A: R.93, N.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.98 NAG.5: 5 residues within 4Å: Chain A: R.305, M.308, N.312, D.410, L.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.305 NAG.6: 4 residues within 4Å: Chain A: P.1338, E.1339, N.1386, D.1389 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.1339

18 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.7: 2 residues within 4Å: Ligands: UNL.9, UNL.12 Ligand excluded by PLIP UNL.8: 2 residues within 4Å: Ligands: UNL.11, UNL.21 Ligand excluded by PLIP UNL.9: 2 residues within 4Å: Chain A: C.1653 Ligands: UNL.7 Ligand excluded by PLIP UNL.10: 4 residues within 4Å: Chain A: A.657, A.658, L.662 Ligands: UNL.11 Ligand excluded by PLIP UNL.11: 3 residues within 4Å: Ligands: UNL.8, UNL.10, UNL.12 Ligand excluded by PLIP UNL.12: 3 residues within 4Å: Ligands: UNL.7, UNL.11, UNL.21 Ligand excluded by PLIP UNL.13: 3 residues within 4Å: Chain A: V.672 Ligands: UNL.14, UNL.16 Ligand excluded by PLIP UNL.14: 5 residues within 4Å: Chain A: F.483, R.548, V.672 Ligands: UNL.13, UNL.17 Ligand excluded by PLIP UNL.15: 2 residues within 4Å: Ligands: UNL.16, UNL.17 Ligand excluded by PLIP UNL.16: 4 residues within 4Å: Chain A: R.482, F.483 Ligands: UNL.13, UNL.15 Ligand excluded by PLIP UNL.17: 4 residues within 4Å: Chain A: L.552 Ligands: UNL.14, UNL.15, UNL.18 Ligand excluded by PLIP UNL.18: 2 residues within 4Å: Chain A: V.545 Ligands: UNL.17 Ligand excluded by PLIP UNL.19: 2 residues within 4Å: Ligands: UNL.22, UNL.23 Ligand excluded by PLIP UNL.20: 1 residues within 4Å: Ligands: UNL.22 Ligand excluded by PLIP UNL.21: 2 residues within 4Å: Ligands: UNL.8, UNL.12 Ligand excluded by PLIP UNL.22: 4 residues within 4Å: Chain A: I.38 Ligands: UNL.19, UNL.20, UNL.24 Ligand excluded by PLIP UNL.23: 1 residues within 4Å: Ligands: UNL.19 Ligand excluded by PLIP UNL.24: 3 residues within 4Å: Chain A: I.38, H.46 Ligands: UNL.22 Ligand excluded by PLIP

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.25: 13 residues within 4Å: Chain A: Q.758, Y.759, F.816, S.819, P.822, A.823, N.843, G.844, A.845, G.846, K.847, T.848, T.849 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.758, A:S.819, A:P.822, A:G.844, A:A.845, A:G.846, A:K.847, A:T.848, A:T.849, A:T.849 pi-Stacking: A:F.816, A:F.816 AGS.26: 10 residues within 4Å: Chain A: Y.1802, A.1809, G.1830, A.1831, G.1832, K.1833, T.1834, S.1835, Q.1874, E.1951 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.1830, A:G.1832, A:K.1833, A:K.1833, A:T.1834, A:T.1834, A:S.1835, A:Q.1874, A:Q.1874 Salt bridges: A:K.1833, A:K.1833

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

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