SMTL ID : 7e7q.1

Cryo-EM structure of human ABCA4 in ATP-bound 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: 5 residues within 4Å: Chain A: L.432, N.436, R.446, L.543, D.544 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA-BMA.2: 7 residues within 4Å: Chain A: P.106, S.111, V.1503, P.1505, N.1550, D.1553, K.1557 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1503

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

NAG.3: 2 residues within 4Å: Chain A: N.119, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.119, A:R.128 NAG.4: 2 residues within 4Å: Chain A: Y.461, N.465 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: A.512, R.521, N.525 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.521 NAG.6: 1 residues within 4Å: Chain A: N.1478 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain A: P.1489, N.1490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1490 NAG.8: 2 residues within 4Å: Chain A: Y.461, N.1609 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.461 NAG.9: 3 residues within 4Å: Chain A: E.552, E.1420, N.1683 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.552 Hydrogen bonds: A:N.1683

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

ATP.10: 16 residues within 4Å: Chain A: F.959, C.962, A.966, N.986, A.988, G.989, K.990, T.991, T.992, Q.1031, H.1139, T.2091, S.2093, G.2095, G.2121 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.986, A:A.988, A:G.989, A:K.990, A:T.991, A:T.991, A:T.992, A:Q.1031, A:G.2095, A:G.2121 Salt bridges: A:K.990, A:K.990, A:H.1139 pi-Stacking: A:F.959, A:F.959 ATP.11: 16 residues within 4Å: Chain A: K.1075, D.1082, S.1084, G.1086, M.1087, Y.1968, N.1995, G.1996, A.1997, G.1998, K.1999, T.2000, T.2001, Q.2040, H.2149 Ligands: MG.13 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.1075, A:S.1084, A:G.1086, A:G.1996, A:G.1996, A:A.1997, A:G.1998, A:K.1999, A:T.2000, A:T.2000, A:T.2001, A:Q.2040, A:Q.2040 Salt bridges: A:K.1999, A:K.1999, A:H.2149 pi-Stacking: A:Y.1968, A:Y.1968

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain A: T.991, Q.1031 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.991 MG.13: 3 residues within 4Å: Chain A: T.2000, Q.2040 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2000

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