MolNFT v1 · #140800 · protein
Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens
5YMT · Outer capsid protein VP4: “Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens”. X-ray diffraction, 3 ligands (GAL, GLC, NAG), 12 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5YMT
- Type
- protein
- Length
- 2,240 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- Q9Q2P6
- Ligands
- GAL, GLC, NAG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Outer capsid protein VP4 | protein | 160 | 10% helix, 56% strand | Q9Q2P6 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains C, D, G
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, C, A, D, G, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.79 | 0.81 | 147 | GAL |
| 2 | 639 | 0.73 | 0.80 | 90 | empty |
| 3 | 127 | 0.66 | 0.89 | 23 | empty |
| 4 | 454 | 0.65 | 0.78 | 62 | empty |
| 5 | 151 | 0.61 | 0.85 | 27 | empty |
Interfaces
18 interfaces between chains.
- G–H · 697 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 542 Ų buried · 11 hydrogen bonds · protein-protein
- G–I · 520 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5YMT · Functional and structural characterization of P[19] rotavirus VP8* interaction with… · 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 Q9Q2P6
- Elsewhere: RCSB PDB 5YMT · PDBe 5YMT · UniProt Q9Q2P6
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