Research workbench
SP2-SP3 - a complex of two storage proteins from bombyx mori hemolymph
Analyse SP2-SP3 - a complex of two storage proteins from bombyx mori hemolymph in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L37
- Type
- protein
- Length
- 1,341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Silkworm storage protein; Arylphorin
- UniProt
- H9JHM9, Q1HPP4
- Ligands
- NAG, MAN, BMA, NA, SCN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Silkworm storage protein | protein | 674 | 42% helix, 19% strand | H9JHM9 |
| B | Arylphorin | protein | 667 | 43% helix, 20% strand | Q1HPP4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NA · Sodium ion · metal · 3 copies · chains A, B
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.82 | 0.93 | 43 | empty |
| 2 | 208 | 0.81 | 0.95 | 41 | empty |
| 3 | 669 | 0.78 | 0.83 | 83 | NAG |
| 4 | 775 | 0.77 | 0.81 | 64 | empty |
| 5 | 278 | 0.75 | 0.87 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2224 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4L37 · SP2-SP3 - a complex of two storage proteins from Bombyx mori hemolymph · 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 H9JHM9
- Every structure of UniProt Q1HPP4
- Elsewhere: RCSB PDB 4L37 · PDBe 4L37 · UniProt H9JHM9 · UniProt Q1HPP4
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