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Structure of the P domain from a GI.7 norovirus variant in complex with lea hbga.
Analyse Structure of the P domain from a GI.7 norovirus variant in complex with lea… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P3I
- Type
- protein
- Length
- 1,143 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
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P domain of VP1 | protein | 290 | 7% helix, 33% strand | G8FL04 |
| B | P domain of VP1 | protein | 282 | 7% helix, 31% strand | G8FL04 |
| C | P domain of VP1 | protein | 282 | 8% helix, 34% strand | G8FL04 |
| D | P domain of VP1 | protein | 289 | 8% helix, 32% strand | G8FL04 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.82 | 0.88 | 90 | empty |
| 2 | 486 | 0.81 | 0.88 | 65 | empty |
| 3 | 53 | 0.66 | 0.96 | 22 | empty |
| 4 | 54 | 0.64 | 0.95 | 24 | empty |
| 5 | 292 | 0.57 | 0.77 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1553 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1508 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 73 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4P3I · Structure of the P domain from a GI.7 Norovirus variant in complex with LeA 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 4P3I · PDBe 4P3I · UniProt G8FL04
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