SMTL ID : 8pko.1

The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: T.286, R.287, L.289, N.303, R.359 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain A: N.899, G.900 Chain B: P.218, Y.221, G.222 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.221

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.573, T.575, R.806 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.765, T.791 Ligands: MAN.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.791, H2O.1, H2O.1, H2O.1

1 x THJ: THIOSULFATE(Non-covalent)

THJ.5: 2 residues within 4Å: Chain A: C.486, G.551 No protein-ligand interaction detected (PLIP)

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

NAG.6: 1 residues within 4Å: Chain A: N.1096 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain B: E.455, E.458, N.460 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.455

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

MAN.7: 9 residues within 4Å: Chain A: D.553, L.648, R.703, P.704, E.705, F.761, T.791, E.792 Ligands: CA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.703, A:E.705, A:T.791 Water bridges: A:T.791, A:T.791, A:T.791

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roversi, P. et al., The ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer). To Be Published

Release Date

2024-07-10

Peptides

Green fluorescent protein,alpha-1,2-Mannosidase: A
Protein disulfide-isomerase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Green fluorescent protein,alpha-1,2-Mannosidase

Protein disulfide-isomerase