SMTL ID : 8k9q.1

Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 20 residues within 4Å: Chain A: N.232, A.281, F.282, S.329, M.330, P.363, V.364, F.366, V.411, V.412, H.445, R.819, T.820, F.822, A.823, V.927, W.1044, P.1047 Ligands: D39.4, D39.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.281, A:F.282, A:V.364, A:F.366, A:V.411, A:T.820, A:F.822, A:A.823, A:V.927, A:W.1044, A:W.1044, A:P.1047 Hydrogen bonds: A:S.329 Salt bridges: A:H.445, A:R.819 Y01.2: 6 residues within 4Å: Chain A: W.145, A.146, I.147, F.152, Y.933, S.937 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.145, A:W.145, A:A.146, A:I.147, A:F.152, A:Y.933, A:Y.933 Y01.3: 7 residues within 4Å: Chain A: I.942, I.946, L.1007, L.1010, G.1011, R.1015, R.1018 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.942, A:L.1007, A:L.1010 Salt bridges: A:R.1015, A:R.1015, A:R.1018

2 x D39: (2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid(Non-covalent)

D39.4: 18 residues within 4Å: Chain A: G.231, N.232, A.233, G.234, Q.238, H.328, S.329, V.411, H.445, Q.446, V.931, L.1043, W.1044, P.1047, L.1050, P.1051 Ligands: Y01.1, D39.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.931, A:W.1044, A:P.1047, A:L.1050, A:P.1051 Hydrogen bonds: A:G.231, A:Q.238, A:Q.238, A:S.329, A:Q.446, A:Q.446 Salt bridges: A:H.328, A:H.445 D39.5: 18 residues within 4Å: Chain A: I.159, L.162, V.165, I.166, V.170, K.177, L.408, T.410, L.814, Y.815, Y.818, F.822, L.919, I.920, I.923, V.930 Ligands: Y01.1, D39.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.162, A:L.162, A:V.165, A:I.166, A:L.814, A:L.814, A:Y.815, A:Y.815, A:Y.818, A:F.822, A:F.822, A:F.822, A:L.919, A:L.919, A:I.920, A:V.930 Hydrogen bonds: A:T.410, A:T.410 Salt bridges: A:K.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, J. et al., Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis. Nat Commun (2024)

Release Date

2023-12-20

Peptides

GPI inositol-deacylase,fused thermostable green fluorescent protein: 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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GPI inositol-deacylase,fused thermostable green fluorescent protein