Research workbench
X-ray structure of melon necrotic spot virus
Analyse X-ray structure of melon necrotic spot virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZAH
- Type
- protein
- Length
- 923 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein
- UniProt
- Q3LHM1
- Ligands
- CA, UNX
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Coat protein | protein | 296 | 7% helix, 46% strand | Q3LHM1 |
| C | Coat protein | protein | 331 | 7% helix, 41% strand | Q3LHM1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.72 | 0.81 | 38 | empty |
| 2 | 422 | 0.64 | 0.78 | 51 | empty |
| 3 | 210 | 0.61 | 0.82 | 37 | empty |
| 4 | 310 | 0.58 | 0.77 | 47 | empty |
| 5 | 233 | 0.53 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 703 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2ZAH · X-ray structure of Melon necrotic spot 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 Q3LHM1
- Elsewhere: RCSB PDB 2ZAH · PDBe 2ZAH · UniProt Q3LHM1
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