SMTL ID : 3ikp.1

Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

10 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.143, N.145, E.151, N.163, D.164 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.143, A:E.151, A:D.164, A:D.164, H2O.1 CA.2: 6 residues within 4Å: Chain A: D.119, E.123, D.146, E.151, D.152 Ligands: CA.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.119, A:D.119, A:D.146, A:D.152, H2O.1 CA.3: 3 residues within 4Å: Chain A: E.123, D.152 Ligands: CA.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.123, A:D.152, H2O.1, H2O.1, H2O.1 CA.4: 3 residues within 4Å: Chain A: E.54 Chain B: E.54 Chain C: E.54 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:E.54, A:E.54, B:E.54, H2O.1, H2O.7, H2O.13 CA.5: 6 residues within 4Å: Chain B: E.143, N.145, E.151, N.163, D.164 Ligands: IPD.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.143, B:E.151, B:D.164, B:D.164 CA.6: 6 residues within 4Å: Chain B: D.119, E.123, D.146, E.151, D.152 Ligands: CA.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.119, B:E.123, B:D.146, B:D.152, H2O.7 CA.7: 3 residues within 4Å: Chain B: E.123, D.152 Ligands: CA.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.123, H2O.7, H2O.8, H2O.10, H2O.10 CA.9: 6 residues within 4Å: Chain C: E.143, N.145, E.151, N.163, D.164 Ligands: IPD.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.143, C:E.151, C:D.164, C:D.164 CA.10: 6 residues within 4Å: Chain C: D.119, E.123, D.146, E.151, D.152 Ligands: CA.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.119, C:E.123, C:D.146, C:D.152, H2O.12 CA.11: 3 residues within 4Å: Chain C: E.123, D.152 Ligands: CA.10 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.123, C:D.152, H2O.12, H2O.13, H2O.16

2 x IPD: D-MYO-INOSITOL-1-PHOSPHATE(Non-covalent)

IPD.8: 7 residues within 4Å: Chain B: E.143, N.145, E.151, N.163, D.164, R.165 Ligands: CA.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.143, B:N.145, B:E.151, B:N.163 Water bridges: B:E.151, B:R.165, B:R.165 Salt bridges: B:R.165 IPD.12: 7 residues within 4Å: Chain C: E.143, N.145, E.151, N.163, D.164, R.165 Ligands: CA.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.143, C:N.145, C:N.163, C:D.164 Salt bridges: C:R.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shrive, A.K. et al., Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325. J.Mol.Biol. (2009)

Release Date

2009-11-17

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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