SMTL ID : 8f5b.1

Human ABCA4 structure in complex with AMP-PNP

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: 8 residues within 4Å: Chain A: L.411, K.412, N.415, F.418, E.419, E.422, R.425, D.523 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.422, A:R.425, A:R.425 NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: S.84, P.85, N.1529, S.1531, D.1532 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: P.87, N.98, R.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.107

2 x MG: MAGNESIUM ION(Post Translational Modification)

MG.4: 4 residues within 4Å: Chain A: S.1063, T.1979, Q.2019 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.1979 MG.5: 3 residues within 4Å: Chain A: T.970, Q.1010 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.970

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 17 residues within 4Å: Chain A: D.1061, L.1062, S.1063, M.1066, Y.1947, V.1973, N.1974, G.1975, A.1976, G.1977, K.1978, T.1979, T.1980, Q.2019, E.2096, H.2128 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.1063, A:S.1063, A:S.1063, A:G.1064, A:N.1974, A:G.1975, A:G.1975, A:A.1976, A:G.1977, A:K.1978, A:K.1978, A:K.1978, A:T.1979, A:T.1980, A:T.1980, A:Q.2019 pi-Stacking: A:Y.1947 ANP.7: 17 residues within 4Å: Chain A: F.938, C.941, N.965, G.966, A.967, G.968, K.969, T.970, T.971, Q.1010, Y.2063, T.2070, Y.2071, S.2072, G.2073, G.2074 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.965, A:G.966, A:G.966, A:K.969, A:K.969, A:K.969, A:T.970, A:T.970, A:T.971, A:Q.1010, A:Q.1010, A:S.2072, A:G.2073, A:G.2074 Salt bridges: A:K.969 pi-Stacking: A:F.938

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scortecci, J.F. et al., Structural and functional characterization of the nucleotide-binding domains of ABCA4 and their role in Stargardt disease. J.Biol.Chem. (2024)

Release Date

2023-11-22

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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