MolNFT v1 · #114548 · protein
Crystal structure of GII.10 P domain in complex with lemon juice
5BSY · Capsid protein: “Crystal structure of GII.10 P domain in complex with lemon juice”. X-ray diffraction, 1 ligand (NO3), 6 pockets (best druggability 0.72). MolNFT v1 #114548 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5BSY
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q5F4T5
- Ligands
- NO3
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 310 | 7% helix, 36% strand | Q5F4T5 |
| B | Capsid protein | protein | 314 | 8% helix, 36% strand | Q5F4T5 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- FLC · Citrate anion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.72 | 0.81 | 73 | empty |
| 2 | 397 | 0.64 | 0.78 | 50 | EDO |
| 3 | 189 | 0.50 | 0.77 | 24 | EDO |
| 4 | 152 | 0.50 | 0.78 | 21 | NO3 |
| 5 | 62 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1973 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5BSY · Crystal structure of GII.10 P domain in complex with lemon juice · 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 5BSY · PDBe 5BSY · UniProt Q5F4T5
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