SMTL ID : 8s3o.1

Structure of native human CD109

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

NAG-NAG.1: 11 residues within 4Å: Chain A: S.1105, D.1106, N.1107, R.1135, A.1136, E.1137, F.1144, W.1145, V.1146, S.1147, S.1148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.1137 NAG-NAG.2: 6 residues within 4Å: Chain A: L.898, T.900, T.1231, G.1232, P.1233, N.1265 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: N.62, T.110, P.112, S.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.62, A:N.62, A:S.113, A:S.113 NAG.4: 4 residues within 4Å: Chain A: N.139, W.660, L.662, T.663 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.662 NAG.5: 4 residues within 4Å: Chain A: N.386, E.452, P.454, S.509 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.386 NAG.6: 4 residues within 4Å: Chain A: R.1331, N.1376, E.1377, T.1378 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.1331, A:R.1331, A:R.1331, A:N.1376, A:T.1378

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almeida, A.V. et al., Three cryo-EM structures of CD109 reveal its mechanism of protease inhibition. Cell Rep (2025)

Release Date

2025-03-05

Peptides

CD109 antigen: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD109 antigen