MolNFT v1 · #158976 · protein
Crystal structure of P[6] rotavirus VP8* complexed with lnfpi
6OAI · Protease-sensitive outer capsid protein: “Crystal structure of P[6] rotavirus VP8* complexed with lnfpi”. X-ray diffraction, 4 ligands (GAL, BGC, NAG), 4 pockets (best druggability 0.81). MolNFT v1 #158976 on GenesisL1: 3D…
- PDB
- 6OAI
- Type
- protein
- Length
- 633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease-sensitive outer capsid protein
- UniProt
- D2DXN5
- Ligands
- GAL, BGC, NAG, FUC
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease-sensitive outer capsid protein | protein | 159 | 10% helix, 57% strand | D2DXN5 |
| B, C, D | Protease-sensitive outer capsid protein | protein | 158 | 8% helix, 58% strand | D2DXN5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B
- BGC · beta-D-glucopyranose · sugar · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.81 | 0.84 | 101 | empty |
| 2 | 630 | 0.79 | 0.85 | 95 | empty |
| 3 | 95 | 0.36 | 0.75 | 22 | empty |
| 4 | 76 | 0.35 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 813 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 796 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 128 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OAI · Crystal structure of P[6] rotavirus vp8* complexed with LNFPI · 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 D2DXN5
- Elsewhere: RCSB PDB 6OAI · PDBe 6OAI · UniProt D2DXN5
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