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Structure of the nuclear factor kappa-B (nf-kb) P50 homodimer
Analyse Structure of the nuclear factor kappa-B (nf-kb) P50 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFK
- Type
- protein + DNA
- Length
- 646 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3'); Protein (nuclear factor kappa-B (nf-kb))
- UniProt
- P25799
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*TP*GP*GP*GP*AP*AP*TP*TP*CP*CP*C)-3') | dna | 11 | — | — |
| A, B | Protein (nuclear factor kappa-B (nf-kb)) | protein | 312 | 13% helix, 32% strand | P25799 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.79 | 0.82 | 100 | empty |
| 2 | 241 | 0.51 | 0.76 | 23 | empty |
| 3 | 81 | 0.45 | 0.81 | 15 | empty |
| 4 | 69 | 0.44 | 0.82 | 16 | empty |
| 5 | 56 | 0.42 | 0.82 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 737 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 670 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–B · 647 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 436 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- D–A · 363 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1NFK · Structure of the nuclear factor kappa-B (nf-kb) P50 homodimer · 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 A 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 P25799
- Elsewhere: RCSB PDB 1NFK · PDBe 1NFK · UniProt P25799
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