Research workbench
Crystal structure of the nucleocapsid protein from schmallenberg virus
Analyse Crystal structure of the nucleocapsid protein from schmallenberg virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZL9
- Type
- protein
- Length
- 903 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid protein
- UniProt
- H2AM13
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid protein | protein | 226 | 56% helix, 7% strand | H2AM13 |
| B | Nucleocapsid protein | protein | 226 | 56% helix, 7% strand | H2AM13 |
| C | Nucleocapsid protein | protein | 227 | 56% helix, 7% strand | H2AM13 |
| D | Nucleocapsid protein | protein | 224 | 57% helix, 7% strand | H2AM13 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.61 | 0.77 | 33 | empty |
| 2 | 289 | 0.57 | 0.76 | 33 | empty |
| 3 | 267 | 0.56 | 0.77 | 33 | empty |
| 4 | 306 | 0.55 | 0.75 | 33 | empty |
| 5 | 156 | 0.44 | 0.75 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1147 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1091 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1080 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1043 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZL9 · Crystal structure of the nucleocapsid protein from Schmallenberg 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 H2AM13
- Elsewhere: RCSB PDB 3ZL9 · PDBe 3ZL9 · UniProt H2AM13
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