MolNFT v1 · #123217 · protein
Binding specificity of P[8] VP8* proteins of rotavirus vaccine strains with histo-blood group antigens
5JDB · Outer capsid protein VP4: “Binding specificity of P[8] VP8* proteins of rotavirus vaccine strains with histo-blood group antigens”. X-ray diffraction, 6 pockets (best druggability 0.89). MolNFT v1 #123217 on GenesisL1: 3D structure…
- PDB
- 5JDB
- Type
- protein
- Length
- 960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- E2EA82
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Outer capsid protein VP4 | protein | 160 | 8% helix, 56% strand | E2EA82 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.89 | 0.90 | 203 | empty |
| 2 | 313 | 0.74 | 0.86 | 68 | empty |
| 3 | 63 | 0.55 | 0.88 | 20 | empty |
| 4 | 52 | 0.55 | 0.89 | 17 | empty |
| 5 | 67 | 0.30 | 0.75 | 14 | empty |
Interfaces
12 interfaces between chains.
- D–F · 502 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 471 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 467 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 460 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JDB · Binding specificity of P[8] VP8* proteins of rotavirus vaccine strains with histo-blood… · 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 E2EA82
- Elsewhere: RCSB PDB 5JDB · PDBe 5JDB · UniProt E2EA82
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