MolNFT v1 · #25280 · protein + DNA
Crystal structure of the nfkb P50/P65 heterodimer complexed to the immunoglobulin kb DNA
1VKX · DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)- 3'): “Crystal structure of the nfkb P50/P65 heterodimer complexed to the immunoglobulin kb DNA”. X-ray diffraction, 6 pockets (best druggability 0.81). MolNFT v1 #25280 on GenesisL1…
- PDB
- 1VKX
- Type
- protein + DNA
- Length
- 609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)- 3'); DNA…
- UniProt
- Q04207, P25799
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*C)- 3') | dna | 12 | — | — |
| D | DNA (5'-D(*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*C)- 3') | dna | 12 | — | — |
| A | Protein (nf-kappa B P65 subunit) | protein | 273 | 7% helix, 29% strand | Q04207 |
| B | Protein (nf-kappa B P50 subunit) | protein | 312 | 12% helix, 29% strand | P25799 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.81 | 0.83 | 102 | empty |
| 2 | 100 | 0.47 | 0.80 | 23 | empty |
| 3 | 124 | 0.44 | 0.77 | 26 | empty |
| 4 | 57 | 0.43 | 0.83 | 16 | empty |
| 5 | 57 | 0.30 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 723 Ų buried · 12 hydrogen bonds · protein-protein
- D–B · 593 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–A · 572 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 496 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–B · 399 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1VKX · Crystal structure of the nfkb P50/P65 heterodimer complexed to the immunoglobulin kb DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P25799 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P25799) · a predicted model of the same protein · chain B 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 Q04207
- Every structure of UniProt P25799
- Elsewhere: RCSB PDB 1VKX · PDBe 1VKX · UniProt Q04207 · UniProt P25799
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