MolNFT v1 · #109590 · protein
Crystal structure of norovirus GII.10 P domain in complex with nano-25
4X7F · Capsid protein: “Crystal structure of norovirus GII.10 P domain in complex with nano-25”. X-ray diffraction, 2 ligands (NA, PO4), 9 pockets (best druggability 0.77). MolNFT v1 #109590 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4X7F
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Nano-25 nanobody
- UniProt
- Q5F4T5
- Ligands
- NA, PO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 307 | 7% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 303 | 7% helix, 37% strand | Q5F4T5 |
| C | Nano-25 nanobody | protein | 114 | 5% helix, 47% strand | — |
| D | Nano-25 nanobody | protein | 112 | 5% helix, 48% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B, C, D
- IMD · Imidazole · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.77 | 0.96 | 33 | IMD |
| 2 | 109 | 0.70 | 0.92 | 19 | empty |
| 3 | 456 | 0.69 | 0.80 | 44 | EDO |
| 4 | 329 | 0.66 | 0.81 | 44 | EDO |
| 5 | 65 | 0.48 | 0.85 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1842 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 867 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4X7F · Crystal structure of norovirus GII.10 P domain in complex with Nano-25 · 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 4X7F · PDBe 4X7F · UniProt Q5F4T5
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