MolNFT v1 · #88650 · protein
Crystal structure of the fiber head domain of the atadenovirus snake adenovirus 1, native, first P212121 crystal form
4D1F · Fiber protein: “Crystal structure of the fiber head domain of the atadenovirus snake adenovirus 1, native, first P212121…”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #88650 on GenesisL1: 3D structure, binding…
- PDB
- 4D1F
- Type
- protein
- Length
- 1,267 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- A9CB96
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, G, H, I, J | Fiber protein | protein | 105 | 8% helix, 60% strand | A9CB96 |
| B, C, F, L | Fiber protein | protein | 106 | 8% helix, 61% strand | A9CB96 |
| K | Fiber protein | protein | 108 | 7% helix, 62% strand | A9CB96 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B, D, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.84 | 0.85 | 105 | empty |
| 2 | 387 | 0.80 | 0.90 | 47 | empty |
| 3 | 366 | 0.80 | 0.90 | 50 | empty |
| 4 | 384 | 0.80 | 0.89 | 50 | empty |
| 5 | 338 | 0.73 | 0.85 | 31 | empty |
Interfaces
30 interfaces between chains.
- B–C · 738 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 730 Ų buried · 9 hydrogen bonds · protein-protein
- J–L · 728 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 725 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 723 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4D1F · Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1… · 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 A9CB96
- Elsewhere: RCSB PDB 4D1F · PDBe 4D1F · UniProt A9CB96
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