Research workbench
Crystal structure of the rhesus rotavirus VP5 antigen domain dimer
Analyse Crystal structure of the rhesus rotavirus VP5 antigen domain dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B4H
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- Q91HI9
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer capsid protein VP4 | protein | 227 | 2% helix, 63% strand | Q91HI9 |
| B | Outer capsid protein VP4 | protein | 218 | 2% helix, 64% strand | Q91HI9 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.72 | 0.76 | 70 | TRS, MPD |
| 2 | 51 | 0.71 | 0.98 | 17 | MPD |
| 3 | 214 | 0.62 | 0.82 | 39 | empty |
| 4 | 83 | 0.50 | 0.83 | 22 | empty |
| 5 | 57 | 0.48 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1926 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2B4H · Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Dimer · 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 Q91HI9
- Elsewhere: RCSB PDB 2B4H · PDBe 2B4H · UniProt Q91HI9
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