Research workbench
The refined structure of nudaurelia capensis omega virus
Analyse The refined structure of nudaurelia capensis omega virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OHF
- Type
- protein
- Length
- 2,263 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudaurelia capensis omega virus capsid protein
- UniProt
- Q90063
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nudaurelia capensis omega virus capsid protein | protein | 539 | 21% helix, 35% strand | Q90063 |
| B | Nudaurelia capensis omega virus capsid protein | protein | 547 | 19% helix, 34% strand | Q90063 |
| C | Nudaurelia capensis omega virus capsid protein | protein | 590 | 21% helix, 32% strand | Q90063 |
| D | Nudaurelia capensis omega virus capsid protein | protein | 587 | 22% helix, 32% strand | Q90063 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.86 | 0.87 | 114 | empty |
| 2 | 1186 | 0.84 | 0.85 | 90 | empty |
| 3 | 1116 | 0.84 | 0.85 | 75 | empty |
| 4 | 222 | 0.80 | 0.94 | 31 | empty |
| 5 | 507 | 0.79 | 0.86 | 86 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3329 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 3093 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2776 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2642 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1850 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1OHF · The refined structure of Nudaurelia capensis omega virus · the same entry in another collection · chain B against B, TM-score 0.96
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 Q90063
- Elsewhere: RCSB PDB 1OHF · PDBe 1OHF · UniProt Q90063
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