SMTL ID : 3dbz.1

human surfactant protein D

Coordinates

PDB Format Compare

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: MPD.5 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.4, H2O.4, H2O.5 CA.6: 5 residues within 4Å: Chain B: E.126, N.128, E.134, N.146, D.147 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.126, B:E.134, B:D.147, B:D.147, H2O.11 CA.7: 6 residues within 4Å: Chain B: D.102, E.106, D.129, E.134, D.135 Ligands: CA.8 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.11 CA.8: 3 residues within 4Å: Chain B: E.106, D.135 Ligands: CA.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.106, H2O.11, H2O.11, H2O.11, H2O.12 CA.9: 5 residues within 4Å: Chain C: E.126, N.128, E.134, N.146, D.147 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.126, C:E.134, C:D.147, C:D.147, H2O.19 CA.10: 6 residues within 4Å: Chain C: D.102, E.106, D.129, E.134, D.135 Ligands: CA.11 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.15 CA.11: 3 residues within 4Å: Chain C: E.106, D.135 Ligands: CA.10 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.106, H2O.15, H2O.19, H2O.19, H2O.19

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MPD.5: 8 residues within 4Å: Chain A: E.126, N.128, D.130, E.134, N.146, D.147, R.148 Ligands: CA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.126, A:N.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Interaction of recombinant surfactant protein D with lipopolysaccharide: conformation and orientation of bound protein by IRRAS and simulations. Biochemistry (2008)

Release Date

2008-08-05

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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