MolNFT v1 · #75872 · protein
Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type H2 (triglycan)
3Q3A · Capsid protein: “Crystal structure of P domain from norwalk virus strain vietnam 026 in complex with hbga type H2 (triglycan)”. X-ray diffraction, 3 ligands (NAG, GAL, FUL), 7 pockets (best druggability 0.73). MolNFT v1 #75872 on…
- PDB
- 3Q3A
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- NAG, GAL, FUL
- Pockets
- 7 · best druggability 0.73
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 | 310 | 7% helix, 36% strand | Q5F4T5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B
- IMD · Imidazole · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.73 | 0.81 | 84 | IMD, EDO |
| 2 | 139 | 0.66 | 0.88 | 26 | EDO |
| 3 | 403 | 0.63 | 0.78 | 48 | EDO |
| 4 | 167 | 0.52 | 0.79 | 21 | IMD |
| 5 | 174 | 0.45 | 0.75 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1881 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3Q3A · 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 3Q3A · PDBe 3Q3A · UniProt Q5F4T5
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