SMTL ID : 7w72.1

Structure of a human glycosylphosphatidylinositol (GPI) transamidase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 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: 4 residues within 4Å: Chain E: N.203, G.206, M.207, Q.208 No protein-ligand interaction detected (PLIP)

1 x 8JY: [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate(Covalent)

8JY.2: 10 residues within 4Å: Chain A: N.383, N.385, F.386, A.389, I.390, L.392 Chain C: D.496, S.498, M.499, L.506 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:A.389, A:I.390, A:L.392, C:L.506 Hydrogen bonds: A:N.383, A:N.385, C:D.496, C:S.498, C:S.498

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

NAG.3: 3 residues within 4Å: Chain B: L.219, N.261, Y.313 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.219 Hydrogen bonds: B:N.261 NAG.4: 4 residues within 4Å: Chain C: T.298, A.299, N.302, R.305 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.302

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain D: D.79, I.82, D.120, S.146 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.79, D:I.82, D:D.120, D:D.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structure of human glycosylphosphatidylinositol transamidase. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-02-16

Peptides

Phosphatidylinositol glycan anchor biosynthesis class U protein: A
GPI transamidase component PIG-S: B
GPI transamidase component PIG-T: C
GPI-anchor transamidase: D
Glycosylphosphatidylinositol anchor attachment 1 protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
U

B
S

C
T

D
K

E
A

Membrane

We predict this structure to be a membrane protein.
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Phosphatidylinositol glycan anchor biosynthesis class U protein

GPI transamidase component PIG-S

GPI transamidase component PIG-T

GPI-anchor transamidase

Glycosylphosphatidylinositol anchor attachment 1 protein