SMTL ID : 2ggx.1

Crystal structure of the trimer neck and carbohydrate recognition domain of human surfactant protein D in complex with p-nitrophenyl maltoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: NPJ.4 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: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.106, A:D.135, A:D.135, H2O.1, H2O.4 CA.5: 6 residues within 4Å: Chain B: E.126, N.128, E.134, N.146, D.147 Ligands: NPJ.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.126, B:E.134, B:D.147, B:D.147 CA.6: 6 residues within 4Å: Chain B: D.102, E.106, D.129, E.134, D.135 Ligands: CA.7 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.7 CA.7: 3 residues within 4Å: Chain B: E.106, D.135 Ligands: CA.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.106, H2O.7, H2O.7, H2O.7, H2O.7 CA.9: 6 residues within 4Å: Chain C: E.126, N.128, E.134, N.146, D.147 Ligands: NPJ.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.126, C:E.134, C:D.147, C:D.147 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.7 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.10, H2O.10, H2O.10, H2O.10

3 x NPJ: 4-NITROPHENYL 4-O-ALPHA-D-GLUCOPYRANOSYL-ALPHA-D-GALACTOPYRANOSIDE(Non-covalent)

NPJ.4: 10 residues within 4Å: Chain A: E.126, N.128, E.134, F.140, T.141, N.142, N.146, D.147, R.148 Ligands: CA.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.126, A:N.128, A:N.142, A:N.146, A:R.148, A:R.148 Water bridges: A:E.138, A:R.154 pi-Stacking: A:F.140 NPJ.8: 11 residues within 4Å: Chain B: E.126, N.128, D.130, E.134, F.140, T.141, N.142, N.146, D.147, R.148 Ligands: CA.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.140 Hydrogen bonds: B:E.126, B:N.128, B:N.142, B:N.146, B:D.147, B:R.148, B:R.148 Water bridges: B:E.126, B:E.126, B:E.138, B:R.154 Salt bridges: B:R.148 pi-Stacking: B:F.140 NPJ.12: 10 residues within 4Å: Chain C: E.126, N.128, E.134, F.140, T.141, N.142, N.146, D.147, R.148 Ligands: CA.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.140 Hydrogen bonds: C:E.126, C:N.128, C:N.142, C:N.146, C:R.148, C:R.148 Water bridges: C:E.126, C:E.126, C:E.138, C:R.154 Salt bridges: C:R.148 pi-Stacking: C:F.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crouch, E. et al., Contributions of Phenylalanine 335 to Ligand Recognition by Human Surfactant Protein D: ring interactions with Sp-D ligands. J.Biol.Chem. (2006)

Release Date

2006-05-02

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

Related Entries With Identical Sequence