MolNFT v1 · #18668 · protein
High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with maltose
1PWB · Pulmonary surfactant-associated protein D: “High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D with…”. X-ray diffraction, 2 ligands (GLC, CA), 3 pockets (best druggability 0.65).…
- PDB
- 1PWB
- Type
- protein
- Length
- 452 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- GLC, CA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% 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, 27% strand | P35247 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.65 | 0.79 | 48 | empty |
| 2 | 147 | 0.50 | 0.78 | 24 | empty |
| 3 | 133 | 0.47 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1094 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1087 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1PWB · High resolution crystal structure of an active recombinant fragment of human lung… · 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 C 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 1PWB · PDBe 1PWB · UniProt P35247
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