Research workbench
Crystal structure of murine nf-kappab inducing kinase (nik) bound to imidazobenzoxepin compound 3
Analyse Crystal structure of murine nf-kappab inducing kinase (nik) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T8O
- Type
- protein
- Length
- 652 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 14
- EC
- 2.7.11.25
- UniProt
- Q9WUL6
- Ligands
- 76Z, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) | protein | 324 | 36% helix, 18% strand | Q9WUL6 |
| B | Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) | protein | 328 | 34% helix, 18% strand | Q9WUL6 |
Ligands and binding sites
- 76Z · 10-(3-methyl-3-oxidanyl-but-1-ynyl)-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.83 | 0.84 | 105 | SO4, 76Z |
| 2 | 261 | 0.70 | 0.85 | 38 | SO4, 76Z |
| 3 | 150 | 0.48 | 0.78 | 22 | empty |
| 4 | 66 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5T8O · Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to Imidazobenzoxepin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WUL6 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 14… · 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 Q9WUL6
- Elsewhere: RCSB PDB 5T8O · PDBe 5T8O · UniProt Q9WUL6
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