Research workbench
Crystal structure of rubella virus capsid protein (residues 127-277)
Analyse Crystal structure of rubella virus capsid protein (residues 127-277) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAR
- Type
- protein
- Length
- 589 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q8QL55
- Ligands
- CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 98 | 11% helix, 45% strand | Q8QL55 |
| B | Capsid protein | protein | 97 | 11% helix, 45% strand | Q8QL55 |
| C | Capsid protein | protein | 100 | 11% helix, 45% strand | Q8QL55 |
| D | Capsid protein | protein | 99 | 11% helix, 44% strand | Q8QL55 |
| E | Capsid protein | protein | 96 | 11% helix, 45% strand | Q8QL55 |
| F | Capsid protein | protein | 99 | 11% helix, 44% strand | Q8QL55 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, D, E
- LDA · Lauryl dimethylamine-N-oxide · additive · 18 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.76 | 0.78 | 55 | LDA |
| 2 | 50 | 0.71 | 0.99 | 17 | CL |
| 3 | 347 | 0.65 | 0.80 | 31 | empty |
| 4 | 126 | 0.40 | 0.75 | 22 | empty |
Interfaces
10 interfaces between chains.
- E–F · 2294 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2267 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2266 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 401 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 391 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4HAR · Crystal Structure of Rubella virus capsid protein (residues 127-277) · 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 Q8QL55
- Elsewhere: RCSB PDB 4HAR · PDBe 4HAR · UniProt Q8QL55
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