MolNFT v1 · #136839 · protein
Otu protease of crimean congo hemorrhagic fever virus bound to ubiquitin variant CC.4
5V5G · RNA-directed RNA polymerase L: “Otu protease of crimean congo hemorrhagic fever virus bound to ubiquitin variant CC.4”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.77). MolNFT v1 #136839 on GenesisL1: 3D…
- 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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