MolNFT v1 · #167909 · protein
Structure of human vaccinia-related kinase 1 (VRK1) bound to LDSM311
6VZH · SERINE/THREONINE-protein kinase VRK1: “Structure of human vaccinia-related kinase 1 (VRK1) bound to LDSM311”. X-ray diffraction, 2 ligands (RYA, SO4), 13 pockets (best druggability 0.70). MolNFT v1 #167909 on GenesisL1: 3D…
- PDB
- 6VZH
- Type
- protein
- Length
- 1,244 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
- RYA, SO4
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 317 | 42% helix, 17% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 301 | 44% helix, 16% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 40% helix, 17% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 311 | 41% helix, 18% strand | Q99986 |
Ligands and binding sites
- RYA · (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.70 | 0.78 | 66 | empty |
| 2 | 702 | 0.69 | 0.77 | 74 | empty |
| 3 | 51 | 0.56 | 0.90 | 18 | empty |
| 4 | 120 | 0.51 | 0.81 | 19 | RYA |
| 5 | 109 | 0.51 | 0.81 | 19 | RYA |
Interfaces
2 interfaces between chains.
- A–B · 206 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 177 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VZH · Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 · 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 6VZH · PDBe 6VZH · UniProt Q99986
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