Research workbench
Crystal structure of the kinase domain of human TRAF2 and nck- interacting protein kinase in complex with compund 9
Analyse Crystal structure of the kinase domain of human TRAF2 and nck- interacting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AX9
- Type
- protein
- Length
- 838 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRAF2 and nck-interacting protein kinase
- EC
- 2.7.11.1
- UniProt
- Q9UKE5
- Ligands
- 4KT, SO4
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 282 | 40% helix, 18% strand | Q9UKE5 |
| B | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 274 | 36% helix, 19% strand | Q9UKE5 |
| C | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 282 | 37% helix, 19% strand | Q9UKE5 |
Ligands and binding sites
- 4KT · 4-methoxy-3-[2-[(3-methoxy-4-morpholin-4-yl-phenyl)amino]pyridin-4-yl]benzenecarbonitrile · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.68 | 0.80 | 36 | empty |
| 2 | 459 | 0.66 | 0.78 | 45 | empty |
| 3 | 400 | 0.66 | 0.79 | 34 | empty |
| 4 | 301 | 0.64 | 0.81 | 36 | empty |
| 5 | 169 | 0.63 | 0.84 | 30 | 4KT |
Interfaces
3 interfaces between chains.
- A–B · 780 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 714 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5AX9 · Crystal structure of the kinase domain of human TRAF2 and NCK-interacting protein kinase… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9UKE5 · AlphaFold monomer V2.0 prediction for TRAF2 and nck-interacting protein kinase (Q9UKE5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9UKE5
- Elsewhere: RCSB PDB 5AX9 · PDBe 5AX9 · UniProt Q9UKE5
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