SMTL ID : 6bbe.1

Structure of N-glycosylated porcine surfactant protein-D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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-NAG-MAN-NAG.1: 4 residues within 4Å: Chain A: N.101, G.107, E.108, P.109 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-NAG.5: 4 residues within 4Å: Chain B: N.101, G.107, E.108, P.109 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-NAG-MAN-NAG.9: 4 residues within 4Å: Chain C: N.101, G.107, E.108, P.109 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.119, N.121, E.130, N.142, D.143 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:E.130, A:D.143, A:D.143 CA.3: 5 residues within 4Å: Chain A: D.95, E.99, N.122, E.130, N.131 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:D.95, A:E.99, A:E.99, H2O.2 CA.6: 5 residues within 4Å: Chain B: E.119, N.121, E.130, N.142, D.143 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.119, B:E.130, B:D.143, B:D.143 CA.7: 5 residues within 4Å: Chain B: D.95, E.99, N.122, E.130, N.131 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, B:D.95, B:E.99, B:E.99, H2O.5 CA.10: 5 residues within 4Å: Chain C: E.119, N.121, E.130, N.142, D.143 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.119, C:E.130, C:D.143, C:D.143 CA.11: 5 residues within 4Å: Chain C: D.95, E.99, N.122, E.130, N.131 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.95, C:D.95, C:E.99, C:E.99, H2O.7

3 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.4: 6 residues within 4Å: Chain A: F.48, E.49, K.50, D.54, V.58 Chain C: A.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50 1PG.8: 6 residues within 4Å: Chain A: A.84 Chain B: F.48, E.49, K.50, D.54, V.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.50 1PG.12: 6 residues within 4Å: Chain B: A.84 Chain C: F.48, E.49, K.50, D.54, V.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Eijk, M. et al., Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus. J. Biol. Chem. (2018)

Release Date

2018-05-23

Peptides

Pulmonary surfactant-associated protein D: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Pulmonary surfactant-associated protein D