SMTL ID : 3g84.1

Crystal structure of the trimeric neck and carbohydrate recognition domain of R343V mutant of human surfactant protein D in complex with alpha 1,2 dimannose.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

MAN-MAN.1: 10 residues within 4Å: Chain A: E.126, N.128, E.134, E.138, N.146, D.147, V.148, E.152, R.154 Ligands: CA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.138, A:N.146, A:E.152, A:R.154 MAN-MAN.2: 11 residues within 4Å: Chain B: E.126, N.128, D.130, E.134, E.138, F.140, N.146, D.147, V.148, R.154 Ligands: CA.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.138, B:N.146, B:R.154 MAN-MAN.3: 11 residues within 4Å: Chain C: E.126, N.128, D.130, E.134, E.138, F.140, N.146, D.147, E.152, R.154 Ligands: CA.10 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.138, C:E.152, C:E.152, C:R.154

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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.126, A:E.134, A:D.147 CA.5: 5 residues within 4Å: Chain A: D.102, E.106, D.129, E.134, D.135 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.102, A:D.102, A:E.106, A:D.129, A:E.134 CA.6: 2 residues within 4Å: Chain A: E.106, D.135 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.106, A:D.135, H2O.1, H2O.1 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: 5 residues within 4Å: Chain B: D.102, E.106, D.129, E.134, D.135 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.102, B:E.106, B:D.129, B:E.134, B:D.135 CA.9: 2 residues within 4Å: Chain B: E.106, D.135 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.106, B:D.135, B:D.135 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: 5 residues within 4Å: Chain C: D.102, E.106, D.129, E.134, D.135 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.102, C:E.106, C:D.129, C:E.134, C:D.135 CA.12: 2 residues within 4Å: Chain C: E.106, D.135 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.106, C:D.135, C:D.135, H2O.5, H2O.5

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