MolNFT v1 · #121565 · protein
Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 fl)
5HZA · Capsid protein: “Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 fl)”. X-ray diffraction, 3 ligands (BGC, FUC, GAL), 6 pockets (best druggability 0.78). MolNFT v1 #121565 on GenesisL1: 3D structure, binding…
- PDB
- 5HZA
- 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
- BGC, FUC, GAL
- Pockets
- 6 · best druggability 0.78
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
- BGC · beta-D-glucopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains B
- EDO · 1,2-ethanediol · additive · 11 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.78 | 0.80 | 133 | EDO |
| 2 | 134 | 0.66 | 0.88 | 23 | EDO |
| 3 | 169 | 0.53 | 0.79 | 28 | EDO |
| 4 | 86 | 0.43 | 0.80 | 22 | EDO |
| 5 | 88 | 0.38 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1891 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5HZA · Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 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 5HZA · PDBe 5HZA · UniProt Q5F4T5
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