SMTL ID : 4m18.1 (3 other biounits)

Crystal Structure of Surfactant Protein-D D325A/R343V mutant in complex with trimannose (Man-a1,2Man-a1,2Man)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-trimer

Ligands

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

MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: E.113, N.115, A.117, E.121, E.125, F.127, N.133, D.134, V.135, R.141 Ligands: CA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.125, A:E.125, A:N.133, A:R.141 MAN-MAN-MAN.2: 11 residues within 4Å: Chain B: E.113, N.115, G.118, E.121, E.125, F.127, N.133, D.134, V.135, R.141 Ligands: CA.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.125, B:N.133, B:R.141

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

MAN-MAN.3: 11 residues within 4Å: Chain C: E.113, N.115, E.121, E.125, F.127, N.133, D.134, V.135, E.139, R.141 Ligands: CA.11 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.125, C:N.133, C:E.139, C:R.141

10 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.113, N.115, E.121, N.133, D.134 Ligands: MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.113, A:E.121, A:D.134, A:D.134 CA.5: 6 residues within 4Å: Chain A: D.89, E.93, D.116, E.121, D.122 Ligands: CA.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.89, A:E.93, A:D.116, A:E.121, A:D.122 CA.6: 3 residues within 4Å: Chain A: E.93, D.122 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.93, A:D.122, A:D.122 CA.7: 5 residues within 4Å: Chain A: E.24, K.38 Chain B: E.24, K.38 Chain C: E.24 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:E.24, C:E.24, B:E.24 CA.8: 6 residues within 4Å: Chain B: E.113, N.115, E.121, N.133, D.134 Ligands: MAN-MAN-MAN.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.113, B:E.121, B:D.134, B:D.134 CA.9: 6 residues within 4Å: Chain B: D.89, E.93, D.116, E.121, D.122 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.89, B:E.93, B:D.116, B:E.121, B:D.122 CA.10: 3 residues within 4Å: Chain B: E.93, D.122 Ligands: CA.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.93, B:D.122, B:D.122 CA.11: 6 residues within 4Å: Chain C: E.113, N.115, E.121, N.133, D.134 Ligands: MAN-MAN.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.113, C:E.121, C:D.134, C:D.134 CA.12: 6 residues within 4Å: Chain C: D.89, E.93, D.116, E.121, D.122 Ligands: CA.13 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.89, C:E.93, C:D.116, C:E.121, C:D.122 CA.13: 3 residues within 4Å: Chain C: E.93, D.122 Ligands: CA.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.93, C:D.122, C:D.122, H2O.1, H2O.1

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Goh, B.C. et al., Molecular mechanisms of inhibition of influenza by surfactant protein d revealed by large-scale molecular dynamics simulation. Biochemistry (2013)

Release Date

2013-12-04

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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