Research workbench
Crystal structure of the human vaccinia-related kinase bound to bi- D1870
Analyse Crystal structure of the human vaccinia-related kinase bound to bi- D1870 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UVF
- Type
- protein
- Length
- 1,230 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
- 7DZ, PO4, CL
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 317 | 40% helix, 17% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 316 | 40% helix, 18% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 301 | 43% helix, 17% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 296 | 42% helix, 17% strand | Q99986 |
Ligands and binding sites
- 7DZ · (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.72 | 0.78 | 67 | empty |
| 2 | 377 | 0.65 | 0.79 | 49 | empty |
| 3 | 64 | 0.60 | 0.90 | 20 | PEG |
| 4 | 63 | 0.59 | 0.90 | 19 | empty |
| 5 | 254 | 0.58 | 0.78 | 29 | 7DZ |
Interfaces
2 interfaces between chains.
- A–C · 262 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 224 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5UVF · Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 · the same entry in another collection · chain D against D, TM-score 1.00
- Q99986 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VRK1 (Q99986) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 5UVF · PDBe 5UVF · UniProt Q99986
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