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Structure of the P domain from a GI.7 norovirus variant in complex with a-type 2 hbga
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- PDB
- 4P26
- Type
- protein
- Length
- 1,150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P domain of VP1
- UniProt
- G8FL04
- Ligands
- NAG, GAL, FUC, A2G
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P domain of VP1 | protein | 292 | 7% helix, 34% strand | G8FL04 |
| B | P domain of VP1 | protein | 285 | 7% helix, 34% strand | G8FL04 |
| C | P domain of VP1 | protein | 289 | 8% helix, 31% strand | G8FL04 |
| D | P domain of VP1 | protein | 284 | 8% helix, 32% strand | G8FL04 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.81 | 0.90 | 56 | empty |
| 2 | 452 | 0.81 | 0.89 | 63 | empty |
| 3 | 234 | 0.62 | 0.82 | 36 | empty |
| 4 | 197 | 0.62 | 0.83 | 34 | empty |
| 5 | 226 | 0.54 | 0.78 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1590 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1498 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4P26 · Structure of the P domain from a GI.7 Norovirus variant in complex with A-type 2 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 4P26 · PDBe 4P26 · UniProt G8FL04
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