Research workbench
The crystal structure of intact afifavidin apo form
Analyse The crystal structure of intact afifavidin apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HDV
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afifavidin
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Afifavidin | protein | 136 | 6% helix, 57% strand | — |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.68 | 0.79 | 58 | empty |
| 2 | 430 | 0.63 | 0.77 | 46 | empty |
| 3 | 293 | 0.58 | 0.78 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1413 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1411 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 409 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 118 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6HDV · The crystal structure of intact afifavidin apo form · 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
- Elsewhere: RCSB PDB 6HDV · PDBe 6HDV
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