Research workbench
Structural mechanism of NEK7 activation by NEK9-induced dimerisation
Analyse Structural mechanism of NEK7 activation by NEK9-induced dimerisation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DE2
- Type
- protein
- Length
- 554 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase NEK7; SERINE/THREONINE-protein kinase NEK9
- EC
- 2.7.11.1
- UniProt
- Q8TDX7, Q8K1R7
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1) | protein | 267 | 41% helix, 17% strand | Q8TDX7 |
| B | SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1) | protein | 262 | 39% helix, 17% strand | Q8TDX7 |
| C | SERINE/THREONINE-protein kinase NEK9 (EC 2.7.11.1) | protein | 16 | 44% helix, 0% strand | Q8K1R7 |
| D | SERINE/THREONINE-protein kinase NEK9 (EC 2.7.11.1) | protein | 9 | 44% helix, 0% strand | Q8K1R7 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.70 | 0.80 | 47 | empty |
| 2 | 449 | 0.70 | 0.80 | 49 | empty |
| 3 | 737 | 0.64 | 0.73 | 62 | empty |
| 4 | 254 | 0.59 | 0.79 | 41 | empty |
| 5 | 120 | 0.44 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 828 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 770 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DE2 · Structural mechanism of Nek7 activation by Nek9-induced dimerisation · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TDX7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK7 (Q8TDX7) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q8K1R7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK9 (Q8K1R7) · a predicted model of the same protein · chain D against A, TM-score 0.78
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 Q8TDX7
- Every structure of UniProt Q8K1R7
- Elsewhere: RCSB PDB 5DE2 · PDBe 5DE2 · UniProt Q8TDX7 · UniProt Q8K1R7
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