Research workbench
Crystal structure of the dimerization domains P50 and relb
Analyse Crystal structure of the dimerization domains P50 and relb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JV4
- Type
- protein
- Length
- 645 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor relb; Nuclear factor nf-kappa-B P105 subunit
- UniProt
- Q04863, P25799
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Transcription factor relb | protein | 101 | 3% helix, 37% strand | Q04863 |
| B, D | Nuclear factor nf-kappa-B P105 subunit | protein | 115 | 3% helix, 40% strand | P25799 |
| F | Nuclear factor nf-kappa-B P105 subunit | protein | 112 | 5% helix, 41% strand | P25799 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.67 | 0.79 | 51 | empty |
| 2 | 186 | 0.53 | 0.78 | 41 | empty |
| 3 | 114 | 0.52 | 0.82 | 21 | empty |
| 4 | 150 | 0.51 | 0.79 | 26 | empty |
| 5 | 110 | 0.39 | 0.75 | 23 | empty |
Interfaces
8 interfaces between chains.
- A–B · 801 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 797 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 756 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 742 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3JV4 · Crystal structure of the dimerization domains p50 and RelB · the same entry in another collection · chain F against F, TM-score 1.00
- Q04863 · AlphaFold monomer V2.0 prediction for transcription factor relb (Q04863) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P25799 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P25799) · a predicted model of the same protein · chain F 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 Q04863
- Every structure of UniProt P25799
- Elsewhere: RCSB PDB 3JV4 · PDBe 3JV4 · UniProt Q04863 · UniProt P25799
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.