MolNFT v1 · #75483 · protein
Structural analysis of a viral otu domain protease from the crimean- congo hemorrhagic fever virus in complex with human ubiquitin
3PRM · L protein: “Structural analysis of a viral otu domain protease from the crimean- congo hemorrhagic fever virus in complex…”. X-ray diffraction, 1 ligand (3CN), 3 pockets (best druggability 0.63). MolNFT v1 #75483 on GenesisL1: 3D…
- PDB
- 3PRM
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L protein; Ubiquitin
- EC
- 3.4.19.12
- UniProt
- Q6TFZ7, P0CG48
- Ligands
- 3CN
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L protein | protein | 161 | 39% helix, 25% strand | Q6TFZ7 |
| B, D | Ubiquitin (EC 3.4.19.12) | protein | 75 | 24% helix, 36% strand | P0CG48 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · 2 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 | 385 | 0.63 | 0.78 | 42 | empty |
| 2 | 158 | 0.49 | 0.77 | 25 | empty |
| 3 | 136 | 0.43 | 0.76 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1073 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1033 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 458 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified, 3 covalent (engineered, covalent ligand).
Compared structures
- 3PRM · Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic… · 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 Q6TFZ7
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 3PRM · PDBe 3PRM · UniProt Q6TFZ7 · UniProt P0CG48
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