Research workbench
Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, native
Analyse Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5O
- Type
- protein
- Length
- 2,049 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LH3 hexon-interlacing capsid protein
- UniProt
- A9CB85
- Ligands
- CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | LH3 hexon-interlacing capsid protein | protein | 338 | 6% helix, 40% strand | A9CB85 |
| B | LH3 hexon-interlacing capsid protein | protein | 345 | 6% helix, 39% strand | A9CB85 |
| C | LH3 hexon-interlacing capsid protein | protein | 342 | 6% helix, 39% strand | A9CB85 |
| E | LH3 hexon-interlacing capsid protein | protein | 348 | 6% helix, 41% strand | A9CB85 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 11 copies · chains A, C, B, D, E, F
- GOL · Glycerol · additive · 8 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.82 | 0.89 | 65 | GOL, ACT |
| 2 | 350 | 0.77 | 0.88 | 40 | empty |
| 3 | 344 | 0.75 | 0.86 | 42 | empty |
| 4 | 271 | 0.72 | 0.86 | 37 | empty |
| 5 | 242 | 0.68 | 0.85 | 33 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1886 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1881 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 1745 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1726 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1724 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5G5O · Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, native · 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 A9CB85
- Elsewhere: RCSB PDB 5G5O · PDBe 5G5O · UniProt A9CB85
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