Research workbench
CHADOX1/ chimpanzee adenovirus Y25 fiber knob protein
Analyse CHADOX1/ chimpanzee adenovirus Y25 fiber knob protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OP2
- Type
- protein
- Length
- 2,216 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber
- UniProt
- G9G864
- Ligands
- CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, G, I, J | Fiber | protein | 187 | 3% helix, 42% strand | G9G864 |
| B, H | Fiber | protein | 181 | 3% helix, 44% strand | G9G864 |
| C | Fiber | protein | 184 | 5% helix, 42% strand | G9G864 |
| K | Fiber | protein | 182 | 5% helix, 43% strand | G9G864 |
| L | Fiber | protein | 179 | 5% helix, 44% strand | G9G864 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, G
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D, F, E, G, I, H, J, K, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.84 | 0.98 | 41 | EDO, TRS |
| 2 | 174 | 0.82 | 0.97 | 37 | EDO |
| 3 | 185 | 0.82 | 0.96 | 42 | EDO |
| 4 | 1182 | 0.82 | 0.83 | 105 | empty |
| 5 | 191 | 0.82 | 0.96 | 41 | EDO |
Interfaces
22 interfaces between chains.
- A–C · 1064 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1037 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1030 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1021 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1021 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7OP2 · Chadox1/ Chimpanzee adenovirus Y25 fiber knob protein · 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 G9G864
- Elsewhere: RCSB PDB 7OP2 · PDBe 7OP2 · UniProt G9G864
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