MolNFT v1 · #140759 · protein
The crystal structure of penaeus vannamei nodavirus P-domain (P21)
5YKZ · Capsid protein: “The crystal structure of penaeus vannamei nodavirus P-domain (P21)”. X-ray diffraction, 1 pocket (best druggability 0.59). MolNFT v1 #140759 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YKZ
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- A5H7Q8
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 112 | 0% helix, 52% strand | A5H7Q8 |
| B | Capsid protein | protein | 114 | 0% helix, 53% strand | A5H7Q8 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.59 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5YKZ · The crystal structure of Penaeus vannamei nodavirus P-domain (P21) · 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 A5H7Q8
- Elsewhere: RCSB PDB 5YKZ · PDBe 5YKZ · UniProt A5H7Q8
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