Research workbench
The crystal structure of SAUGI/KSHVUDG complex
Analyse The crystal structure of SAUGI/KSHVUDG complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYV
- Type
- protein
- Length
- 2,660 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Human herpesvirus 8; Staphylococcus aureus
- Molecule
- Uracil-DNA glycosylase; Saugi
- EC
- 3.2.2.27
- UniProt
- Q76RG8, Q936H5
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.7 · 8 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 234 | 41% helix, 11% strand | Q76RG8 |
| B, D, J, P | Saugi | protein | 100 | 29% helix, 37% strand | Q936H5 |
| E | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 234 | 41% helix, 11% strand | Q76RG8 |
| F, N | Saugi | protein | 97 | 28% helix, 38% strand | Q936H5 |
| G | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 233 | 41% helix, 12% strand | Q76RG8 |
| H, L | Saugi | protein | 99 | 27% helix, 37% strand | Q936H5 |
| I, M, O | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 233 | 41% helix, 12% strand | Q76RG8 |
| K | Uracil-DNA glycosylase (EC 3.2.2.27) | protein | 234 | 41% helix, 12% strand | Q76RG8 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.77 | 0.82 | 63 | empty |
| 2 | 833 | 0.73 | 0.78 | 87 | empty |
| 3 | 852 | 0.71 | 0.76 | 87 | empty |
| 4 | 859 | 0.68 | 0.74 | 64 | empty |
| 5 | 417 | 0.64 | 0.78 | 56 | empty |
Interfaces
29 interfaces between chains.
- A–B · 1479 Ų buried · 21 hydrogen bonds · protein-protein
- K–L · 1468 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1467 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1440 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1440 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6LYV · The crystal structure of SAUGI/KSHVUDG complex · 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 Q76RG8
- Every structure of UniProt Q936H5
- Elsewhere: RCSB PDB 6LYV · PDBe 6LYV · UniProt Q76RG8 · UniProt Q936H5
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