Research workbench
Crystal structure of human nf-kappab inducing kinase (nik)
Analyse Crystal structure of human nf-kappab inducing kinase (nik) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G3D
- Type
- protein
- Length
- 1,215 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nf-kappa-beta-inducing kinase
- EC
- 2.7.11.25
- UniProt
- Q99558
- Ligands
- MG
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nf-kappa-beta-inducing kinase (EC 2.7.11.25) | protein | 324 | 35% helix, 17% strand | Q99558 |
| B | Nf-kappa-beta-inducing kinase (EC 2.7.11.25) | protein | 318 | 34% helix, 17% strand | Q99558 |
| D | Nf-kappa-beta-inducing kinase (EC 2.7.11.25) | protein | 290 | 34% helix, 18% strand | Q99558 |
| E | Nf-kappa-beta-inducing kinase (EC 2.7.11.25) | protein | 283 | 35% helix, 19% strand | Q99558 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.81 | 0.82 | 116 | empty |
| 2 | 358 | 0.68 | 0.81 | 49 | MG |
| 3 | 289 | 0.66 | 0.82 | 37 | MG |
| 4 | 198 | 0.64 | 0.84 | 26 | MG |
| 5 | 347 | 0.56 | 0.75 | 40 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1231 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 370 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4G3D · Crystal structure of human NF-kappaB inducing kinase (NIK) · the same entry in another collection · chain E against E, TM-score 1.00
- Q99558 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 14… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q99558
- Elsewhere: RCSB PDB 4G3D · PDBe 4G3D · UniProt Q99558
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