MolNFT v1 · #121566 · protein
Crystal structure of GII.10 P domain in complex with 2-fucosyllactose (2'FL)
5HZB · Capsid protein: “Crystal structure of GII.10 P domain in complex with 2-fucosyllactose (2'FL)”. X-ray diffraction, 3 ligands (GLC, GAL, FUC), 5 pockets (best druggability 0.74). MolNFT v1 #121566 on GenesisL1: 3D structure, binding…
- PDB
- 5HZB
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- GLC, GAL, FUC
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 314 | 8% helix, 38% strand | Q5F4T5 |
| B | Capsid protein | protein | 307 | 7% helix, 36% strand | Q5F4T5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.74 | 0.83 | 79 | empty |
| 2 | 149 | 0.64 | 0.86 | 25 | empty |
| 3 | 355 | 0.58 | 0.76 | 50 | empty |
| 4 | 167 | 0.52 | 0.79 | 25 | EDO |
| 5 | 78 | 0.44 | 0.81 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 1901 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5HZB · Crystal structure of GII.10 P domain in complex with 2-fucosyllactose (2'FL) · 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 5HZB · PDBe 5HZB · UniProt Q5F4T5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.