MolNFT v1 · #179858 · protein
Crystal structure of P[6] rotavirus VP8* in complex with lnt
7KI5 · Capsid protein: “Crystal structure of P[6] rotavirus VP8* in complex with lnt”. X-ray diffraction, 3 ligands (GAL, BGC, NAG), 3 pockets (best druggability 0.80). MolNFT v1 #179858 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7KI5
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q91E88
- Ligands
- GAL, BGC, NAG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Capsid protein | protein | 158 | 10% helix, 58% strand | Q91E88 |
| C | Capsid protein | protein | 157 | 8% helix, 56% strand | Q91E88 |
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
- GOL · Glycerol · additive · 2 copies · chains A, C, D
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.80 | 0.84 | 104 | GOL |
| 2 | 688 | 0.78 | 0.83 | 106 | GOL |
| 3 | 88 | 0.36 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 784 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 784 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 606 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 134 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KI5 · Crystal structure of P[6] rotavirus vp8* in complex with LNT · 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 Q91E88
- Elsewhere: RCSB PDB 7KI5 · PDBe 7KI5 · UniProt Q91E88
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