MolNFT v1 · #10231 · protein
IKAPPABALPHA/NF-kappab complex
1IKN · Protein (nf-kappa-B P65 subunit): “IKAPPABALPHA/NF-kappab complex”. X-ray diffraction, 11 pockets (best druggability 0.70). MolNFT v1 #10231 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IKN
- Type
- protein
- Length
- 609 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (nf-kappa-B P65 subunit); Protein (nf-kappa-B P50D subunit); Protein…
- UniProt
- Q04207, P25799, P25963
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (nf-kappa-B P65 subunit) | protein | 282 | 6% helix, 37% strand | Q04207 |
| C | Protein (nf-kappa-B P50D subunit) | protein | 112 | 3% helix, 44% strand | P25799 |
| D | Protein (I-kappa-B-alpha) | protein | 215 | 39% helix, 0% strand | P25963 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.70 | 0.86 | 39 | empty |
| 2 | 409 | 0.67 | 0.80 | 50 | empty |
| 3 | 666 | 0.67 | 0.76 | 57 | empty |
| 4 | 82 | 0.58 | 0.87 | 26 | empty |
| 5 | 155 | 0.55 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1240 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 777 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 742 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1IKN · IKAPPABALPHA/NF-kappab complex · the same entry in another collection · chain A against A, TM-score 1.00
- P25799 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P25799) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P25963 · AlphaFold monomer V2.0 prediction for nf-kappa-B inhibitor alpha (P25963) · a predicted model of the same protein · chain D against A, TM-score 0.92
- Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.66
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 Q04207
- Every structure of UniProt P25799
- Every structure of UniProt P25963
- Elsewhere: RCSB PDB 1IKN · PDBe 1IKN · UniProt Q04207 · UniProt P25799 · UniProt P25963
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