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Structure of the P domain from a GI.7 norovirus variant in complex with ley hbga.
Analyse Structure of the P domain from a GI.7 norovirus variant in complex with ley… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P25
- Type
- protein
- Length
- 1,153 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- G8FL04
- Ligands
- FUC, NAG, GAL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein | protein | 288 | 7% helix, 33% strand | G8FL04 |
| B | Major capsid protein | protein | 288 | 7% helix, 34% strand | G8FL04 |
| C | Major capsid protein | protein | 288 | 8% helix, 33% strand | G8FL04 |
| D | Major capsid protein | protein | 289 | 9% helix, 33% strand | G8FL04 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.82 | 0.87 | 90 | empty |
| 2 | 714 | 0.79 | 0.83 | 81 | empty |
| 3 | 199 | 0.65 | 0.85 | 45 | empty |
| 4 | 222 | 0.63 | 0.82 | 35 | empty |
| 5 | 122 | 0.55 | 0.83 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1513 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1477 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 218 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4P25 · Structure of the P domain from a GI.7 Norovirus variant in complex with LeY 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 G8FL04
- Elsewhere: RCSB PDB 4P25 · PDBe 4P25 · UniProt G8FL04
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