Research workbench
Crystal structure of the fiber head domain of the atadenovirus snake adenovirus 1, selenomethionine-derivative
Analyse Crystal structure of the fiber head domain of the atadenovirus snake adenovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D0U
- Type
- protein
- Length
- 427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- A9CB96
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 108 | 7% helix, 60% strand | A9CB96 |
| B | Fiber protein | protein | 105 | 8% helix, 60% strand | A9CB96 |
| C | Fiber protein | protein | 106 | 8% helix, 61% strand | A9CB96 |
| D | Fiber protein | protein | 108 | 7% helix, 61% strand | A9CB96 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, C
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.79 | 0.86 | 65 | empty |
| 2 | 441 | 0.61 | 0.76 | 34 | PE8 |
| 3 | 134 | 0.43 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 785 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 697 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 230 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 115 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4D0U · 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 4D0U · PDBe 4D0U · UniProt A9CB96
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