Research workbench
Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, methylmercury chloride derivative
Analyse Structure of the snake adenovirus 1 hexon-interlacing LH3 protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5N
- Type
- protein
- Length
- 1,022 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LH3 hexon-interlacing capsid protein
- UniProt
- A9CB85
- Ligands
- MMC, CL
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LH3 hexon-interlacing capsid protein | protein | 338 | 6% helix, 40% strand | A9CB85 |
| B | LH3 hexon-interlacing capsid protein | protein | 341 | 6% helix, 40% strand | A9CB85 |
| C | LH3 hexon-interlacing capsid protein | protein | 343 | 6% helix, 39% strand | A9CB85 |
Ligands and binding sites
- MMC · Methyl mercury ion · ligand · 10 copies · chains A, C, B
- CL · Chloride ion · ion · 14 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.67 | 0.82 | 35 | empty |
| 2 | 262 | 0.54 | 0.77 | 40 | CL, MMC |
| 3 | 249 | 0.53 | 0.76 | 34 | MMC, CL |
| 4 | 108 | 0.45 | 0.79 | 30 | MMC |
| 5 | 117 | 0.41 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1790 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1706 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1639 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5G5N · Structure of the snake adenovirus 1 hexon-interlacing LH3 protein, methylmercury chloride… · 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 5G5N · PDBe 5G5N · UniProt A9CB85
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