MolNFT v1 · #39915 · protein + DNA
Structure of nf-kb P65-P50 heterodimer bound to prdii element of B- interferon promoter
2I9T · 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)- 3': “Structure of nf-kb P65-P50 heterodimer bound to prdii element of B- interferon promoter”. X-ray diffraction, 5 pockets (best druggability 0.85). MolNFT v1 #39915 on…
- PDB
- 2I9T
- Type
- protein + DNA
- Length
- 621 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)- 3'…
- UniProt
- Q04207, P25799
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)- 3' | dna | 17 | — | — |
| D | 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)- 3' | dna | 17 | — | — |
| A | Transcription factor P65 | protein | 275 | 9% helix, 37% strand | Q04207 |
| B | Nuclear factor nf-kappa-B P105 subunit | protein | 312 | 16% helix, 37% strand | P25799 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.85 | 0.86 | 75 | empty |
| 2 | 101 | 0.55 | 0.84 | 19 | empty |
| 3 | 63 | 0.49 | 0.85 | 19 | empty |
| 4 | 103 | 0.44 | 0.79 | 24 | empty |
| 5 | 77 | 0.42 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 761 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–B · 757 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 638 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 477 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–B · 297 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2I9T · Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter · 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 0.95
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 2I9T · PDBe 2I9T · UniProt Q04207 · UniProt P25799
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