Research workbench
The crystal structure of the DNA binding domain of virf-1 from the oncogenic kshv
Analyse The crystal structure of the DNA binding domain of virf-1 from the oncogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HLX
- Type
- protein
- Length
- 397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K9
- UniProt
- Q77Q82
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | K9 | protein | 99 | 34% helix, 21% strand | Q77Q82 |
| B | K9 | protein | 100 | 35% helix, 21% strand | Q77Q82 |
| C, D | K9 | protein | 99 | 35% helix, 21% strand | Q77Q82 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.62 | 0.74 | 52 | empty |
| 2 | 61 | 0.33 | 0.77 | 12 | empty |
| 3 | 89 | 0.29 | 0.71 | 16 | empty |
| 4 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 301 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 231 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HLX · The crystal structure of the DNA binding domain of vIRF-1 from the oncogenic KSHV · 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 Q77Q82
- Elsewhere: RCSB PDB 4HLX · PDBe 4HLX · UniProt Q77Q82
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