Research workbench
Crystal structure of norovirus GII.10 P domain in complex with nano-85
Analyse Crystal structure of norovirus GII.10 P domain in complex with nano-85 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X7E
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nano-85 nanobody
- UniProt
- Q5F4T5
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 304 | 7% helix, 37% strand | Q5F4T5 |
| C | Nano-85 nanobody | protein | 121 | 5% helix, 57% strand | — |
| B | Capsid protein | protein | 302 | 7% helix, 37% strand | Q5F4T5 |
| D | Nano-85 nanobody | protein | 120 | 5% helix, 58% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.78 | 0.80 | 112 | EDO, ACT |
| 2 | 172 | 0.55 | 0.80 | 28 | empty |
| 3 | 64 | 0.37 | 0.79 | 20 | empty |
| 4 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1897 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 755 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 738 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4X7E · Crystal structure of norovirus GII.10 P domain in complex with Nano-85 · 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 4X7E · PDBe 4X7E · UniProt Q5F4T5
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