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Structure of the P domain from a GI.7 norovirus variant in complex with H-type 2 hbga
Analyse Structure of the P domain from a GI.7 norovirus variant in complex with H-type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P1V
- Type
- protein
- Length
- 1,150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P domain of vpi
- UniProt
- G8FL04
- Ligands
- NAG, GAL, FUC
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P domain of vpi | protein | 289 | 8% helix, 32% strand | G8FL04 |
| B | P domain of vpi | protein | 280 | 8% helix, 32% strand | G8FL04 |
| C | P domain of vpi | protein | 291 | 7% helix, 34% strand | G8FL04 |
| D | P domain of vpi | protein | 290 | 7% helix, 33% 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.84 | 0.85 | 120 | empty |
| 2 | 1117 | 0.78 | 0.80 | 114 | empty |
| 3 | 76 | 0.67 | 0.93 | 24 | empty |
| 4 | 120 | 0.57 | 0.84 | 31 | empty |
| 5 | 180 | 0.55 | 0.80 | 35 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1575 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1530 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 546 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 147 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4P1V · Structure of the P domain from a GI.7 Norovirus variant in complex with H-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 4P1V · PDBe 4P1V · UniProt G8FL04
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