SMTL ID : 2rib.1

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with L-glycero-D-manno-heptose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.126, N.128, E.134, N.146, D.147 Ligands: GMH.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.126, A:E.134, A:D.147, A:D.147 CA.2: 6 residues within 4Å: Chain A: D.102, E.106, D.129, E.134, D.135 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.102, A:D.102, A:E.106, A:D.129, A:D.135 CA.3: 3 residues within 4Å: Chain A: E.106, D.135 Ligands: CA.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.106, A:D.135, H2O.6, H2O.6, H2O.6 CA.5: 6 residues within 4Å: Chain B: E.126, N.128, E.134, N.146, D.147 Ligands: GMH.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.126, B:E.134, B:D.147, B:D.147 CA.6: 6 residues within 4Å: Chain B: D.102, E.106, D.129, E.134, D.135 Ligands: CA.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.102, B:E.106, B:D.129, B:D.135, H2O.12 CA.7: 3 residues within 4Å: Chain B: E.106, D.135 Ligands: CA.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.106, H2O.12, H2O.12, H2O.12, H2O.13 CA.9: 6 residues within 4Å: Chain C: E.126, N.128, E.134, N.146, D.147 Ligands: GMH.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.126, C:E.134, C:D.147, C:D.147 CA.10: 5 residues within 4Å: Chain C: D.102, E.106, D.129, E.134, D.135 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.102, C:E.106, C:D.129, C:D.135, H2O.17 CA.11: 2 residues within 4Å: Chain C: E.106, D.135 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.106, H2O.16, H2O.18, H2O.18, H2O.18

3 x GMH: L-glycero-alpha-D-manno-heptopyranose(Non-covalent)

GMH.4: 8 residues within 4Å: Chain A: E.126, N.128, D.130, E.134, N.146, D.147, R.148 Ligands: CA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.126, A:N.128, A:E.134, A:N.146 Water bridges: A:D.130, A:R.148 GMH.8: 8 residues within 4Å: Chain B: E.126, N.128, D.130, E.134, N.146, D.147, R.148 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.126, B:N.128, B:E.134, B:N.146 Water bridges: B:D.130 GMH.12: 8 residues within 4Å: Chain C: E.126, N.128, D.130, E.134, N.146, D.147, R.148 Ligands: CA.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.126, C:E.126, C:N.128, C:E.134, C:N.146 Water bridges: C:R.148

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d. Biochemistry (2008)

Release Date

2008-01-15

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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