SMTL ID : 8ee6.1

Cryo-EM Structure of human ABCA7 in PE/Ch nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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: E.1285, H.1313, N.1381, T.1383 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 2 residues within 4Å: Chain A: N.1518, L.1716 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-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.2: 5 residues within 4Å: Chain A: E.1339, S.1340, P.1341, N.1386, D.1389 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1341

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

NAG.4: 3 residues within 4Å: Chain A: N.78, T.80, L.279 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.80 Hydrogen bonds: A:T.80 NAG.5: 4 residues within 4Å: Chain A: R.93, N.98, R.1422, P.1424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.93, A:R.1422, A:R.1422 NAG.6: 4 residues within 4Å: Chain A: N.312, E.316, L.409, D.410 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.312, A:E.316 NAG.7: 1 residues within 4Å: Chain A: N.1335 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain A: E.317, R.1453, K.1456, N.1457, A.1460 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.1460 Hydrogen bonds: A:R.1453, A:R.1453

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

UNL.9: 1 residues within 4Å: Chain A: A.658 Ligand excluded by PLIP UNL.10: 3 residues within 4Å: Chain A: G.661, L.662 Ligands: UNL.16 Ligand excluded by PLIP UNL.11: 4 residues within 4Å: Chain A: V.545, L.552 Ligands: UNL.19, UNL.23 Ligand excluded by PLIP UNL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.13: 1 residues within 4Å: Ligands: UNL.17 Ligand excluded by PLIP UNL.14: 1 residues within 4Å: Ligands: UNL.16 Ligand excluded by PLIP UNL.15: 2 residues within 4Å: Chain A: T.1646 Ligands: UNL.28 Ligand excluded by PLIP UNL.16: 3 residues within 4Å: Chain A: Y.560 Ligands: UNL.10, UNL.14 Ligand excluded by PLIP UNL.17: 1 residues within 4Å: Ligands: UNL.13 Ligand excluded by PLIP UNL.18: 5 residues within 4Å: Chain A: F.483, R.548, A.676, K.1407 Ligands: UNL.27 Ligand excluded by PLIP UNL.19: 3 residues within 4Å: Chain A: R.548, V.672 Ligands: UNL.11 Ligand excluded by PLIP UNL.20: 1 residues within 4Å: Ligands: UNL.22 Ligand excluded by PLIP UNL.21: 3 residues within 4Å: Chain A: R.482, F.483 Ligands: UNL.22 Ligand excluded by PLIP UNL.22: 3 residues within 4Å: Chain A: M.1664 Ligands: UNL.20, UNL.21 Ligand excluded by PLIP UNL.23: 2 residues within 4Å: Chain A: V.42 Ligands: UNL.11 Ligand excluded by PLIP UNL.24: 1 residues within 4Å: Ligands: UNL.25 Ligand excluded by PLIP UNL.25: 1 residues within 4Å: Ligands: UNL.24 Ligand excluded by PLIP UNL.26: 2 residues within 4Å: Chain A: W.677, W.1408 Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Ligands: UNL.18 Ligand excluded by PLIP UNL.28: 4 residues within 4Å: Chain A: L.655, V.1649, C.1653 Ligands: UNL.15 Ligand excluded by PLIP

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

AGS.29: 11 residues within 4Å: Chain A: Q.758, Y.759, F.816, S.819, A.823, N.843, G.844, G.846, K.847, T.848, T.849 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.758, A:Q.758, A:G.844, A:A.845, A:G.846, A:K.847, A:T.848, A:T.848, A:T.849, A:T.849 pi-Stacking: A:F.816, A:F.816 AGS.30: 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:Y.1802, A:G.1830, A:G.1832, A:K.1833, A:T.1834, A:T.1834, A:S.1835, A:Q.1874, A:E.1951 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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