SMTL ID : 3g83.1

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 9 residues within 4Å: Chain A: E.126, N.128, D.130, E.134, F.140, N.146, D.147, R.148 Ligands: CA.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.126, A:N.128, A:N.146, A:N.146 Water bridges: A:D.130, A:D.130, A:D.130, A:R.148 MAN-MAN.2: 9 residues within 4Å: Chain B: E.126, N.128, D.130, E.134, F.140, N.146, D.147, R.148 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.126, B:N.128, B:E.134, B:N.146 MAN-MAN.3: 9 residues within 4Å: Chain C: E.126, N.128, D.130, E.134, F.140, N.146, D.147, R.148 Ligands: CA.10 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.126, C:N.128, C:E.134, C:N.146 Water bridges: C:R.148, C:R.148

9 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.126, N.128, E.134, N.146, D.147 Ligands: MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.126, A:E.134, A:D.147, A:D.147 CA.5: 6 residues within 4Å: Chain A: D.102, E.106, D.129, E.134, D.135 Ligands: CA.6 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.6: 3 residues within 4Å: Chain A: E.106, D.135 Ligands: CA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.106, A:D.135, H2O.1, H2O.2, H2O.6 CA.7: 6 residues within 4Å: Chain B: E.126, N.128, E.134, N.146, D.147 Ligands: MAN-MAN.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.126, B:E.134, B:D.147, B:D.147 CA.8: 6 residues within 4Å: Chain B: D.102, E.106, D.129, E.134, D.135 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.102, B:D.102, B:E.106, B:D.129, B:D.135 CA.9: 3 residues within 4Å: Chain B: E.106, D.135 Ligands: CA.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.106, H2O.12, H2O.13, H2O.14, H2O.14 CA.10: 6 residues within 4Å: Chain C: E.126, N.128, E.134, N.146, D.147 Ligands: MAN-MAN.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.126, C:E.134, C:D.147, C:D.147 CA.11: 6 residues within 4Å: Chain C: D.102, E.106, D.129, E.134, D.135 Ligands: CA.12 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.12: 3 residues within 4Å: Chain C: E.106, D.135 Ligands: CA.11 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.106, H2O.20, H2O.20, H2O.20, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crouch, E. et al., Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Biochemistry (2009)

Release Date

2009-03-17

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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