SMTL ID : 8k9t.1

Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 13 residues within 4Å: Chain A: N.232, A.281, F.282, A.329, M.330, P.363, V.364, V.411, V.412, R.819, F.822 Ligands: LYI.6, CLR.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.232, A:A.281, A:F.282, A:V.364, A:V.411 Hydrogen bonds: A:N.232, A:M.330 Salt bridges: A:H.445

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

MAN.2: 7 residues within 4Å: Chain A: K.177, D.444, Q.446, A.447, W.450 Ligands: MAN.3, 80Y.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.177, A:K.177, A:D.444, A:D.444, A:Q.446, A:A.447 MAN.3: 4 residues within 4Å: Chain A: Q.446 Ligands: MAN.2, 05E.4, 80Y.9 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.4: 7 residues within 4Å: Chain A: S.235, K.237, R.240, E.277 Ligands: MAN.3, PA1.5, 80Y.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.235, A:S.235, A:R.240, A:R.240, A:E.277 Salt bridges: A:K.237

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

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

1 x LYI: [(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] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate(Non-covalent)

LYI.6: 26 residues within 4Å: Chain A: L.162, V.165, I.166, G.231, N.232, A.233, G.234, Q.238, H.328, A.329, T.410, V.411, H.445, Q.446, L.814, Y.815, Y.818, R.819, F.822, I.920, I.923, I.934, L.1043 Ligands: PLM.1, PA1.5, CLR.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.162, A:V.165, A:I.166, A:Y.815, A:Y.815, A:F.822, A:I.920, A:I.923, A:I.934, A:I.934, A:L.1043 Hydrogen bonds: A:G.231, A:N.232, A:Q.238, A:H.445, A:Q.446

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 6 residues within 4Å: Chain A: W.145, F.152, S.155, T.929, V.930, Y.933 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.145, A:W.145, A:F.152, A:F.152, A:T.929, A:V.930, A:Y.933, A:Y.933, A:Y.933 CLR.8: 10 residues within 4Å: Chain A: N.232, I.279, F.282, L.1043, W.1044, P.1047, L.1050, P.1051 Ligands: PLM.1, LYI.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.282, A:F.282, A:F.282, A:L.1043, A:W.1044, A:P.1047, A:L.1050, A:L.1050, A:P.1051 Hydrogen bonds: A:N.232

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.9: 9 residues within 4Å: Chain A: M.181, S.182, R.240, P.241, W.450 Chain B: S.272 Ligands: MAN.2, MAN.3, 05E.4 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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