SMTL ID : 5oxr.1

Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R7 oligosaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

2 x K5B- GMH- GMH: L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-4,7-anhydro-3-deoxy-D-gluco-oct-2-ulosonic acid

K5B-GMH-GMH.1: 8 residues within 4Å: Chain B: E.143, N.145, D.147, E.151, N.163, D.164, R.165 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.165, B:R.165 Water bridges: B:D.147 Salt bridges: B:R.165 K5B-GMH-GMH.2: 8 residues within 4Å: Chain C: E.143, N.145, D.147, E.151, N.163, D.164, R.165 Ligands: CA.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.165, C:R.165 Salt bridges: C:R.165

9 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: E.143, N.145, E.151, N.163, D.164 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.143, A:E.151, A:D.164, A:D.164, H2O.1 CA.4: 6 residues within 4Å: Chain A: D.119, E.123, D.146, E.151, D.152 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.119, A:D.119, A:E.123, A:D.146, A:D.152 CA.5: 3 residues within 4Å: Chain A: E.123, D.152 Ligands: CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.123, A:D.152, A:D.152, H2O.4, H2O.4 CA.6: 6 residues within 4Å: Chain B: E.143, N.145, E.151, N.163, D.164 Ligands: K5B-GMH-GMH.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.143, B:E.151, B:D.164, B:D.164 CA.7: 6 residues within 4Å: Chain B: D.119, E.123, D.146, E.151, D.152 Ligands: CA.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.119, B:E.123, B:D.146, B:D.152, H2O.9 CA.8: 3 residues within 4Å: Chain B: E.123, D.152 Ligands: CA.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.123, H2O.10, H2O.10, H2O.12, H2O.12 CA.9: 6 residues within 4Å: Chain C: E.143, N.145, E.151, N.163, D.164 Ligands: K5B-GMH-GMH.2 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.143, C:E.151, C:D.164, C:D.164 CA.10: 6 residues within 4Å: Chain C: D.119, E.123, D.146, E.151, D.152 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.119, C:D.119, C:E.123, C:D.146, C:D.152 CA.11: 3 residues within 4Å: Chain C: E.123, D.152 Ligands: CA.10 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.123, H2O.16, H2O.16, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Littlejohn, J.R. et al., Structural definition of hSP-D recognition of Salmonella enterica LPS inner core oligosaccharides reveals alternative binding modes for the same LPS. PLoS ONE (2018)

Release Date

2018-06-20

Peptides

Pulmonary surfactant-associated protein D: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Pulmonary surfactant-associated protein D

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