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Crystal structure of neoculin, a sweet protein with taste-modifying activity.
Analyse Crystal structure of neoculin, a sweet protein with taste-modifying activity. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D04
- Type
- protein
- Length
- 888 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neoculin acidic subunit; Curculin
- UniProt
- P19667
- Ligands
- NAG, BMA, FUL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Neoculin acidic subunit | protein | 111 | 0% helix, 42% strand | — |
| B, D, H | Curculin | protein | 111 | 0% helix, 43% strand | P19667 |
| C | Neoculin acidic subunit | protein | 113 | 0% helix, 40% strand | — |
| F | Curculin | protein | 110 | 0% helix, 45% strand | P19667 |
| G | Neoculin acidic subunit | protein | 110 | 0% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains G, D, A
- BMA · beta-D-mannopyranose · sugar · chains H
- FUL · beta-L-fucopyranose · sugar · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.76 | 0.78 | 104 | empty |
| 2 | 594 | 0.69 | 0.78 | 51 | empty |
| 3 | 348 | 0.53 | 0.73 | 46 | empty |
| 4 | 131 | 0.47 | 0.78 | 24 | empty |
| 5 | 117 | 0.45 | 0.78 | 23 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1295 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1265 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1252 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 481 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P19667
- Elsewhere: RCSB PDB 2D04 · PDBe 2D04 · UniProt P19667
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