Research workbench
Crystal structure of a nf-kb heterodimer bound to the IG/HIV-kb siti
Analyse Crystal structure of a nf-kb heterodimer bound to the IG/HIV-kb siti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LE9
- Type
- protein + DNA
- Length
- 1,218 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3'; 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3'…
- UniProt
- Q04207, P25799
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | 5'-D(*TP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*T)-3' | dna | 12 | — | — |
| D, H | 5'-D(*AP*AP*GP*GP*AP*AP*AP*GP*TP*CP*CP*C)-3' | dna | 12 | — | — |
| A, E | Nuclear factor nf-kappa-B P65 subunit | protein | 273 | 5% helix, 33% strand | Q04207 |
| B, F | Nuclear factor nf-kappa-B P50 subunit | protein | 312 | 10% helix, 31% strand | P25799 |
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.84 | 0.85 | 101 | empty |
| 2 | 1102 | 0.83 | 0.85 | 82 | empty |
| 3 | 270 | 0.53 | 0.76 | 37 | empty |
| 4 | 70 | 0.45 | 0.83 | 19 | empty |
| 5 | 73 | 0.42 | 0.80 | 20 | empty |
Interfaces
13 interfaces between chains.
- A–E · 1042 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 716 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 10 hydrogen bonds · protein-protein
- D–B · 636 Ų buried · 10 hydrogen bonds · protein-nucleic
- H–F · 607 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1LE9 · Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti · the same entry in another collection · chain F against F, 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 B against A, TM-score 0.97
- Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 1LE9 · PDBe 1LE9 · UniProt Q04207 · UniProt P25799
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