Research workbench
Crystal structure of cucumber necrosis virus
Analyse Crystal structure of cucumber necrosis virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LLF
- Type
- protein
- Length
- 4,505 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P15183
- Ligands
- CA, ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H, K, N | Capsid protein | protein | 289 | 5% helix, 47% strand | P15183 |
| B, F, I, L, O | Capsid protein | protein | 291 | 5% helix, 46% strand | P15183 |
| D, G, J, M, P | Capsid protein | protein | 321 | 4% helix, 46% strand | P15183 |
Ligands and binding sites
- CA · Calcium ion · metal · 15 copies · chains A, B, D, E, G, F, H, J, I, K, M, L, N, P, O
- ZN · Zinc ion · metal · 5 copies · chains D, G, J, M, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.81 | 0.85 | 87 | empty |
| 2 | 653 | 0.80 | 0.85 | 90 | CA |
| 3 | 390 | 0.77 | 0.87 | 58 | empty |
| 4 | 390 | 0.75 | 0.85 | 52 | empty |
| 5 | 362 | 0.73 | 0.84 | 45 | CA |
Interfaces
35 interfaces between chains.
- I–K · 1904 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1904 Ų buried · 16 hydrogen bonds · protein-protein
- A–O · 1899 Ų buried · 15 hydrogen bonds · protein-protein
- L–N · 1899 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 1887 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4LLF · Crystal structure of Cucumber Necrosis Virus · 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 P15183
- Elsewhere: RCSB PDB 4LLF · PDBe 4LLF · UniProt P15183
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