Research workbench
Crystal structure of human vaccinia-related kinase 1 (VRK1) in complex with AMP-pnp
Analyse Crystal structure of human vaccinia-related kinase 1 (VRK1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AC9
- Type
- protein
- Length
- 1,246 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
- ANP, MG, SO4, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 317 | 39% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 316 | 40% helix, 19% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 307 | 41% helix, 20% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 306 | 42% helix, 19% strand | Q99986 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D, B
- GOL · Glycerol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.74 | 0.77 | 86 | SO4, GOL |
| 2 | 652 | 0.70 | 0.78 | 58 | PG4, GOL |
| 3 | 73 | 0.66 | 0.93 | 19 | empty |
| 4 | 66 | 0.63 | 0.92 | 19 | empty |
| 5 | 151 | 0.50 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–D · 646 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 595 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AC9 · Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP · 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 C 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 6AC9 · PDBe 6AC9 · UniProt Q99986
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