Research workbench
Crystal structure of the human vaccinia-related kinase bound to a bis- difluorophenol-aminopyridine inhibitor
Analyse Crystal structure of the human vaccinia-related kinase bound to a bis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BU6
- Type
- protein
- Length
- 1,262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase VRK1
- EC
- 2.7.11.1
- UniProt
- Q99986
- Ligands
- E8V, CL, SO4
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 322 | 38% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 307 | 40% helix, 19% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 40% helix, 19% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 318 | 42% helix, 20% strand | Q99986 |
Ligands and binding sites
- E8V · 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol) · ligand · 3 copies · chains A, B, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.72 | 0.77 | 80 | SO4 |
| 2 | 696 | 0.71 | 0.77 | 63 | SO4 |
| 3 | 219 | 0.65 | 0.83 | 31 | E8V |
| 4 | 191 | 0.64 | 0.84 | 33 | E8V |
| 5 | 165 | 0.60 | 0.83 | 24 | E8V |
Interfaces
2 interfaces between chains.
- A–B · 266 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 180 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BU6 · Crystal Structure of the Human vaccinia-related kinase bound to a… · 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 Q99986
- Elsewhere: RCSB PDB 6BU6 · PDBe 6BU6 · UniProt Q99986
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