MolNFT v1 · #61526 · protein + DNA
X-ray structure of a nf-kb P52/RELB/DNA complex
3DO7 · Avian reticuloendotheliosis viral (V-rel) oncogene related B: “X-ray structure of a nf-kb P52/RELB/DNA complex”. X-ray diffraction, 8 pockets (best druggability 0.83). MolNFT v1 #61526 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DO7
- Type
- protein + DNA
- Length
- 621 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avian reticuloendotheliosis viral (V-rel) oncogene related B; Nuclear factor nf-kappa-B…
- UniProt
- Q8VE46, Q00653
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Avian reticuloendotheliosis viral (V-rel) oncogene related B | protein | 296 | 5% helix, 29% strand | Q8VE46 |
| B | Nuclear factor nf-kappa-B P100 subunit | protein | 293 | 12% helix, 27% strand | Q00653 |
| C | 5'- D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3' | dna | 10 | — | — |
| D, E | 5'- D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3' | dna | 11 | — | — |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.83 | 0.85 | 92 | empty |
| 2 | 76 | 0.76 | 0.97 | 21 | empty |
| 3 | 106 | 0.68 | 0.91 | 26 | empty |
| 4 | 220 | 0.55 | 0.78 | 34 | empty |
| 5 | 171 | 0.49 | 0.77 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 780 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 601 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 505 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 408 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–D · 302 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 Q8VE46
- Every structure of UniProt Q00653
- Elsewhere: RCSB PDB 3DO7 · PDBe 3DO7 · UniProt Q8VE46 · UniProt Q00653
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