Research workbench
Structure of the C-terminal head domain of the avian adenovirus EDSV fiber
Analyse Structure of the C-terminal head domain of the avian adenovirus EDSV fiber in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ITX
- Type
- protein
- Length
- 1,313 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Duck adenovirus 1
- Molecule
- Fiber protein
- UniProt
- S4TZM6
- Ligands
- GLN, SO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.75 · 5 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 219 | 8% helix, 41% strand | S4TZM6 |
| B | Fiber protein | protein | 216 | 10% helix, 44% strand | S4TZM6 |
| D | Fiber protein | protein | 223 | 6% helix, 41% strand | S4TZM6 |
| C, E | Fiber protein | protein | 217 | 7% helix, 40% strand | S4TZM6 |
| F | Fiber protein | protein | 221 | 9% helix, 41% strand | S4TZM6 |
Ligands and binding sites
- GLN · Glutamine · ligand · 5 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.84 | 0.96 | 33 | SO4 |
| 2 | 216 | 0.83 | 0.97 | 33 | SO4 |
| 3 | 616 | 0.70 | 0.79 | 77 | SO4 |
| 4 | 342 | 0.65 | 0.80 | 32 | empty |
| 5 | 372 | 0.64 | 0.78 | 42 | GLN |
Interfaces
9 interfaces between chains.
- D–F · 1101 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1096 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1049 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 965 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ITX · Structure of the C-terminal head domain of the avian adenovirus edsv fiber · 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 S4TZM6
- Elsewhere: RCSB PDB 6ITX · PDBe 6ITX · UniProt S4TZM6
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