Research workbench
Crystal structure of the fiber head domain of the atadenovirus snake adenovirus 1, native, second P212121 crystal form
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
- 4D1G
- Type
- protein
- Length
- 1,285 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- A9CB96
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 107 | 7% helix, 62% strand | A9CB96 |
| B, G, I | Fiber protein | protein | 108 | 7% helix, 62% strand | A9CB96 |
| C, D, F, H, K, L | Fiber protein | protein | 107 | 7% helix, 62% strand | A9CB96 |
| E, J | Fiber protein | protein | 106 | 8% helix, 61% strand | A9CB96 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains B, E, K, C, D, G, F, H, J, A, I, L
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 6 copies · chains B, C, D, E, A, G, I, F, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.79 | 0.86 | 63 | empty |
| 2 | 540 | 0.78 | 0.85 | 63 | empty |
| 3 | 527 | 0.78 | 0.85 | 61 | empty |
| 4 | 582 | 0.76 | 0.83 | 63 | SO4 |
| 5 | 519 | 0.74 | 0.82 | 38 | PE8 |
Interfaces
30 interfaces between chains.
- G–H · 757 Ų buried · 9 hydrogen bonds · protein-protein
- J–L · 755 Ų buried · 8 hydrogen bonds · protein-protein
- G–I · 754 Ų buried · 7 hydrogen bonds · protein-protein
- H–I · 754 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 754 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4D1G · Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1… · the same entry in another collection · chain F against F, 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 4D1G · PDBe 4D1G · UniProt A9CB96
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