Research workbench
Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D
Analyse Crystal structure of inositol phosphate bound trimeric human lung surfactant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKP
- Type
- protein
- Length
- 453 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pulmonary surfactant-associated protein D
- UniProt
- P35247
- Ligands
- IPD, CA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pulmonary surfactant-associated protein D | protein | 151 | 36% helix, 25% strand | P35247 |
| B | Pulmonary surfactant-associated protein D | protein | 152 | 37% helix, 25% strand | P35247 |
| C | Pulmonary surfactant-associated protein D | protein | 150 | 36% helix, 25% strand | P35247 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 2 copies · chains B, C
- CA · Calcium ion · metal · 10 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.66 | 0.80 | 52 | CA |
| 2 | 135 | 0.50 | 0.79 | 20 | empty |
| 3 | 114 | 0.44 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1071 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1052 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1011 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3IKP · Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D · 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 B 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 3IKP · PDBe 3IKP · UniProt P35247
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