SMTL ID : 4e52.1

Crystal structure of Haemophilus Eagan 4A polysaccharide bound human lung surfactant protein D

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

2 x GMH- KD5: 4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic acid-(5-1)-L-glycero-alpha-D-manno-heptopyranose(Non-covalent)

GMH-KD5.1: 8 residues within 4Å: Chain B: E.143, N.145, D.147, E.151, N.163, D.164, R.165 Ligands: CA.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.143, B:N.145, B:E.151, B:N.163, B:D.147 GMH-KD5.2: 8 residues within 4Å: Chain C: E.143, N.145, D.147, E.151, N.163, D.164, R.165 Ligands: CA.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.143, C:E.143, C:N.145, C:E.151, C:N.163, C:D.147

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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.143, A:E.151, A:D.164, H2O.1, 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.119, A:E.123, A:D.146, A:D.152, H2O.1 CA.5: 3 residues within 4Å: Chain A: E.123, D.152 Ligands: CA.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.123, A:D.152, H2O.1, H2O.1, H2O.2 CA.6: 6 residues within 4Å: Chain B: E.143, N.145, E.151, N.163, D.164 Ligands: GMH-KD5.1 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.8 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.8, H2O.8, H2O.10, H2O.11 CA.9: 6 residues within 4Å: Chain C: E.143, N.145, E.151, N.163, D.164 Ligands: GMH-KD5.2 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.15, H2O.15, H2O.15, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, H.W. et al., Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains. Infect.Immun. (2016)

Release Date

2013-03-27

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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