SMTL ID : 8k9r.1

Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.1: 7 residues within 4Å: Chain A: K.177, D.444, Q.446, A.447, W.450 Ligands: MAN.2, 80Y.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.177, A:Q.446 MAN.2: 4 residues within 4Å: Chain A: Q.446 Ligands: MAN.1, 05E.3, 80Y.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.446

1 x 05E: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate(Non-covalent)

05E.3: 7 residues within 4Å: Chain A: S.235, K.237, R.240, E.277 Ligands: MAN.2, PA1.4, 80Y.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.235, A:S.235, A:R.240, A:R.240

1 x PA1: 2-amino-2-deoxy-alpha-D-glucopyranose(Non-covalent)

PA1.4: 6 residues within 4Å: Chain A: A.233, Q.238, E.277, Q.446 Ligands: 05E.3, L9H.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.233, A:E.277

1 x L9H: [(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate(Non-covalent)

L9H.5: 26 residues within 4Å: Chain A: L.162, V.165, G.231, N.232, A.233, G.234, Q.238, F.282, H.328, S.329, T.410, V.411, N.445, L.814, Y.815, Y.818, R.819, F.822, I.920, I.923, L.1043, W.1044, P.1047, L.1050 Ligands: PA1.4, PLM.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.162, A:V.165, A:F.282, A:L.814, A:Y.815, A:Y.815, A:Y.818, A:F.822, A:I.920, A:I.923, A:W.1044, A:P.1047, A:L.1050 Hydrogen bonds: A:G.231, A:Q.238, A:S.329, A:S.329, A:N.445

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 15 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, R.819, T.820, F.822, A.823 Ligands: L9H.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.281, A:F.282, A:F.282, A:V.364, A:F.366, A:V.411, A:T.820, A:F.822, A:A.823 Hydrogen bonds: A:S.329, A:N.445

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 7 residues within 4Å: Chain A: W.145, F.152, S.155, L.156, I.159, V.930, Y.933 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.145, A:F.152, A:L.156, A:I.159, A:V.930, A:Y.933

1 x 80Y: 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate(Non-covalent)

80Y.8: 9 residues within 4Å: Chain A: M.181, S.182, M.184, R.240, W.450 Chain B: S.272 Ligands: MAN.1, MAN.2, 05E.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.182, B:S.272 Salt bridges: A:R.240

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,MCherry protein: A
Green fluorescent protein,Complement decay-accelerating factor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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GPI inositol-deacylase,MCherry protein

Green fluorescent protein,Complement decay-accelerating factor

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