Research workbench
Crystal structure of bombyx mori SP2/SP3 heterohexamer
Analyse Crystal structure of bombyx mori SP2/SP3 heterohexamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WJM
- Type
- protein
- Length
- 4,016 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arylphorin; Silkworm storage protein
- UniProt
- Q1HPP4, H9JHM9
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arylphorin | protein | 670 | 43% helix, 19% strand | Q1HPP4 |
| B, C | Silkworm storage protein | protein | 668 | 41% helix, 19% strand | H9JHM9 |
| D | Silkworm storage protein | protein | 672 | 40% helix, 19% strand | H9JHM9 |
| E, F | Arylphorin | protein | 669 | 42% helix, 19% strand | Q1HPP4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, E, B, D, C, F
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains A, B, F, C
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, D, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.86 | 0.88 | 97 | NAG |
| 2 | 550 | 0.85 | 0.90 | 57 | empty |
| 3 | 851 | 0.84 | 0.86 | 79 | empty |
| 4 | 627 | 0.84 | 0.88 | 68 | empty |
| 5 | 189 | 0.83 | 0.97 | 33 | empty |
Interfaces
12 interfaces between chains.
- B–F · 2144 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 2138 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2124 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1163 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1138 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 3WJM · Crystal structure of Bombyx mori Sp2/Sp3 heterohexamer · 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 Q1HPP4
- Every structure of UniProt H9JHM9
- Elsewhere: RCSB PDB 3WJM · PDBe 3WJM · UniProt Q1HPP4 · UniProt H9JHM9
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