Research workbench
Crystal structure of GII.10 P domain in complex with 150MM fucose
Analyse Crystal structure of GII.10 P domain in complex with 150MM fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z4S
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- FUL, NO3
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 314 | 8% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 312 | 7% helix, 35% strand | Q5F4T5 |
Ligands and binding sites
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B
- NO3 · Nitrate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.80 | 0.81 | 117 | EDO |
| 2 | 146 | 0.60 | 0.84 | 25 | empty |
| 3 | 162 | 0.51 | 0.79 | 26 | EDO |
| 4 | 52 | 0.26 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4Z4S · Crystal structure of GII.10 P domain in complex with 150mM fucose · 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 4Z4S · PDBe 4Z4S · UniProt Q5F4T5
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