Research workbench
Crystal structure of the viral otu domain protease from taggert virus
Analyse Crystal structure of the viral otu domain protease from taggert virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DX3
- Type
- protein
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- A0A142J8F6
- Ligands
- MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 161 | 37% helix, 27% strand | A0A142J8F6 |
| B | RNA-dependent RNA polymerase | protein | 164 | 36% helix, 26% strand | A0A142J8F6 |
| C | RNA-dependent RNA polymerase | protein | 163 | 36% helix, 26% strand | A0A142J8F6 |
| D | RNA-dependent RNA polymerase | protein | 164 | 37% helix, 26% strand | A0A142J8F6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.81 | 0.84 | 91 | empty |
| 2 | 778 | 0.80 | 0.83 | 76 | empty |
| 3 | 100 | 0.36 | 0.75 | 20 | empty |
| 4 | 74 | 0.33 | 0.76 | 20 | empty |
| 5 | 58 | 0.31 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- B–D · 900 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 869 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DX3 · Crystal structure of the viral OTU domain protease from Taggert virus · the same entry in another collection · chain D against D, 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 A0A142J8F6
- Elsewhere: RCSB PDB 6DX3 · PDBe 6DX3 · UniProt A0A142J8F6
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