MolNFT v1 · #75871 · protein
Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type H2 (diglycan)
3Q39 · Capsid protein: “Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type H2 (diglycan)”. X-ray diffraction, 2 ligands (GAL, FUC), 6 pockets (best druggability 0.75). MolNFT v1 #75871 on…
- PDB
- 3Q39
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- GAL, FUC
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 315 | 8% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 307 | 7% helix, 37% strand | Q5F4T5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 571 | 0.75 | 0.82 | 70 | EDO |
| 2 | 458 | 0.68 | 0.79 | 50 | EDO |
| 3 | 141 | 0.63 | 0.86 | 25 | empty |
| 4 | 180 | 0.53 | 0.79 | 25 | EDO |
| 5 | 52 | 0.29 | 0.75 | 11 | EDO |
Interfaces
1 interface between chains.
- A–B · 1902 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3Q39 · Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA… · 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 Q5F4T5
- Elsewhere: RCSB PDB 3Q39 · PDBe 3Q39 · UniProt Q5F4T5
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