Research workbench
crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with myoinositol
Analyse crystal structure of the trimeric neck and carbohydrate recognition domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OS9
- Type
- protein
- Length
- 452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Homo sapiens
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- INS, CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pulmonary surfactant-associated protein D | protein | 151 | 36% helix, 25% strand | P35247 |
| C | Pulmonary surfactant-associated protein D | protein | 150 | 36% helix, 25% strand | P35247 |
Ligands and binding sites
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.58 | 0.80 | 32 | empty |
| 2 | 132 | 0.46 | 0.77 | 22 | empty |
| 3 | 129 | 0.46 | 0.77 | 23 | empty |
| 4 | 111 | 0.43 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1108 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1097 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1059 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2OS9 · Crystal structure of the trimeric neck and carbohydrate recognition domain of human… · the same entry in another collection · chain A against A, TM-score 1.00
- P35247 · AlphaFold monomer V2.0 prediction for pulmonary surfactant-associated protein D (P35247) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P35247
- Elsewhere: RCSB PDB 2OS9 · PDBe 2OS9 · UniProt P35247
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