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   PDBe-KB   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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