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Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand salmonella enterica minnesota R5 oligosaccharide
Analyse Crystal structure of human lung surfactant protein D trimeric fragment with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OXS
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- K5B, GMH, GLC, CA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulmonary surfactant-associated protein D | protein | 152 | 37% helix, 25% strand | P35247 |
| B, C | Pulmonary surfactant-associated protein D | protein | 153 | 37% helix, 25% strand | P35247 |
Ligands and binding sites
- K5B · 4,7-anhydro-3-deoxy-D-gluco-oct-2-ulosonic acid · ligand · 3 copies · chains B, C
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 6 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 5 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.59 | 0.81 | 32 | empty |
| 2 | 159 | 0.53 | 0.80 | 22 | empty |
| 3 | 164 | 0.49 | 0.77 | 23 | empty |
| 4 | 133 | 0.46 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1168 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1094 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5OXS · Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand… · the same entry in another collection · chain A against A, TM-score 1.00
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 5OXS · PDBe 5OXS · UniProt P35247
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