MolNFT v1 · #57269 · protein
Crystal structure of ginkbilobin-2, the novel antifungal protein from ginkgo biloba seeds
3A2E: “Crystal structure of ginkbilobin-2, the novel antifungal protein from ginkgo biloba seeds”. X-ray diffraction, 4 pockets (best druggability 0.51). MolNFT v1 #57269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A2E
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ginkbilobin-2
- UniProt
- A4ZDL6
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ginkbilobin-2 | protein | 108 | 31% helix, 30% strand | A4ZDL6 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.51 | 0.81 | 23 | empty |
| 2 | 149 | 0.48 | 0.77 | 21 | empty |
| 3 | 158 | 0.42 | 0.74 | 29 | empty |
| 4 | 89 | 0.37 | 0.76 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 630 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 622 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 115 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3A2E · Crystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds · the same entry in another collection · chain A against A, TM-score 1.00
- A4ZDL6 · AlphaFold monomer V2.0 prediction for antifungal protein ginkbilobin-2 (A4ZDL6) · a predicted model of the same protein · chain A 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 A4ZDL6
- Elsewhere: RCSB PDB 3A2E · PDBe 3A2E · UniProt A4ZDL6
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