Research workbench
Otu protease of crimean congo hemorrhagic fever virus bound to ubiquitin variant CC.4
Analyse Otu protease of crimean congo hemorrhagic fever virus bound to ubiquitin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V5G
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase L; Ubiquitin variant CC.4
- EC
- 3.4.19.12, 2.7.7.48
- UniProt
- Q6TQR6
- Ligands
- NA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA-directed RNA polymerase L (EC 3.4.19.12, 2.7.7.48) | protein | 165 | 39% helix, 24% strand | Q6TQR6 |
| B | Ubiquitin variant CC.4 | protein | 80 | 23% helix, 35% strand | — |
| D | Ubiquitin variant CC.4 | protein | 80 | 19% helix, 35% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.77 | 0.79 | 77 | empty |
| 2 | 64 | 0.41 | 0.81 | 16 | EDO |
| 3 | 84 | 0.40 | 0.78 | 22 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1036 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5V5G · OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.4 · 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 Q6TQR6
- Elsewhere: RCSB PDB 5V5G · PDBe 5V5G · UniProt Q6TQR6
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