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Crystal structure of the kinase domain of TRAF2 and nck-interacting protein kinase with ncb-0846
Analyse Crystal structure of the kinase domain of TRAF2 and nck-interacting protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D7A
- Type
- protein
- Length
- 861 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
- 58C, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 289 | 39% helix, 17% strand | Q9UKE5 |
| B | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 286 | 37% helix, 17% strand | Q9UKE5 |
| C | TRAF2 and nck-interacting protein kinase (EC 2.7.11.1) | protein | 286 | 35% helix, 17% strand | Q9UKE5 |
Ligands and binding sites
- 58C · Cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.77 | 0.79 | 107 | 58C |
| 2 | 521 | 0.72 | 0.80 | 36 | SO4 |
| 3 | 499 | 0.69 | 0.79 | 55 | 58C |
| 4 | 264 | 0.66 | 0.83 | 40 | 58C |
| 5 | 448 | 0.63 | 0.77 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1492 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 817 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- Q9UKE5 · AlphaFold monomer V2.0 prediction for TRAF2 and nck-interacting protein kinase (Q9UKE5) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 5D7A · PDBe 5D7A · UniProt Q9UKE5
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