MolNFT v1 · #89364 · protein
Crystal structure of nf-kb-inducing kinase (nik)
4DN5 · Mitogen-activated protein kinase kinase kinase 14: “Crystal structure of nf-kb-inducing kinase (nik)”. X-ray diffraction, 2 ligands (AGS, MG), 6 pockets (best druggability 0.79). MolNFT v1 #89364 on GenesisL1: 3D structure, binding…
- PDB
- 4DN5
- Type
- protein
- Length
- 661 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
- Q99558
- Ligands
- AGS, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% 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 | 331 | 35% helix, 18% strand | Q99558 |
| B | Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) | protein | 330 | 34% helix, 19% strand | Q99558 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.79 | 0.81 | 90 | MG, EDO, AGS |
| 2 | 941 | 0.78 | 0.80 | 91 | MG, EDO, AGS |
| 3 | 68 | 0.70 | 0.96 | 20 | empty |
| 4 | 155 | 0.50 | 0.79 | 23 | empty |
| 5 | 78 | 0.44 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1564 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4DN5 · Crystal Structure of NF-kB-inducing Kinase (NIK) · the same entry in another collection · chain A against A, 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 B 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 4DN5 · PDBe 4DN5 · UniProt Q99558
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