Research workbench
Crystal structure of GII.10 P domain in complex with 7.5MM B antigen (trisaccharide)
Analyse Crystal structure of GII.10 P domain in complex with 7.5MM B antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z4Y
- 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
- GLA, FUC
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 315 | 8% helix, 37% strand | Q5F4T5 |
| B | Capsid protein | protein | 307 | 7% helix, 37% strand | Q5F4T5 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains B, A
- FUC · alpha-L-fucopyranose · sugar · chains A, B
- EDO · 1,2-ethanediol · additive · 9 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 | 604 | 0.75 | 0.82 | 76 | EDO |
| 2 | 463 | 0.67 | 0.79 | 57 | EDO |
| 3 | 135 | 0.63 | 0.86 | 25 | empty |
| 4 | 157 | 0.52 | 0.79 | 25 | EDO |
| 5 | 77 | 0.33 | 0.75 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 1876 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4Z4Y · Crystal structure of GII.10 P domain in complex with 7.5mM B antigen (trisaccharide) · 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 4Z4Y · PDBe 4Z4Y · UniProt Q5F4T5
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