SMTL ID : 7e7i.1

Cryo-EM structure of human ABCA4 in the apo state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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.1: 9 residues within 4Å: Chain A: R.386, L.432, K.433, N.436, E.440, E.443, R.446, L.543, D.544 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.443 NAG-NAG-BMA-BMA-BMA.2: 8 residues within 4Å: Chain A: S.105, P.106, P.112, Q.1502, V.1503, P.1505, N.1550, D.1553 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: I.114, N.119, R.128 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.114 NAG.4: 1 residues within 4Å: Chain A: N.465 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.465 NAG.5: 2 residues within 4Å: Chain A: R.521, N.525 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.525 NAG.6: 1 residues within 4Å: Chain A: N.1478 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.1490 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: Y.461, N.1609 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.461 Hydrogen bonds: A:Y.461 NAG.9: 2 residues within 4Å: Chain A: E.1420, N.1683 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1683

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)(Covalent)

3PE.10: 8 residues within 4Å: Chain A: Q.42, I.44, W.52, I.685, S.689, A.783, F.791 Ligands: 3PE.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.52, A:I.685, A:F.791 Salt bridges: A:H.1038 3PE.11: 18 residues within 4Å: Chain A: L.781, A.784, C.785, F.791, T.792, H.1386, K.1392, D.1393, L.1395, A.1396, L.1400, F.1404, L.1720, Q.1724, S.1810, Y.1813, V.1814 Ligands: 3PE.10 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.781, A:A.784, A:F.791, A:L.1395, A:L.1395, A:A.1396, A:L.1400, A:F.1404, A:Y.1813, A:V.1814, A:V.1814 Hydrogen bonds: A:H.1386, A:Q.1724 Salt bridges: A:K.1392, A:K.1392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Structural basis of substrate recognition and translocation by human ABCA4. Nat Commun (2021)

Release Date

2021-06-30

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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