MolNFT v1 · #106997 · protein
Crystal structure of dioscorin from dioscorea japonica
4TWM · Dioscorin 5: “Crystal structure of dioscorin from dioscorea japonica”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.69). MolNFT v1 #106997 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4TWM
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioscorin 5
- UniProt
- A7MAQ2
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioscorin 5 | protein | 239 | 20% helix, 37% strand | A7MAQ2 |
| B | Dioscorin 5 | protein | 236 | 17% helix, 37% strand | A7MAQ2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.69 | 0.78 | 55 | empty |
| 2 | 157 | 0.53 | 0.79 | 22 | empty |
| 3 | 123 | 0.51 | 0.80 | 18 | empty |
| 4 | 94 | 0.34 | 0.74 | 18 | empty |
| 5 | 73 | 0.32 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 A7MAQ2
- Elsewhere: RCSB PDB 4TWM · PDBe 4TWM · UniProt A7MAQ2
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