Research workbench
Crystal structure of the dimerization domains P52 homodimer
Analyse Crystal structure of the dimerization domains P52 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JV5
- Type
- protein
- Length
- 411 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear factor nf-kappa-B P100 subunit
- UniProt
- Q9WTK5
- Pockets
- 1 · best druggability 0.44
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear factor nf-kappa-B P100 subunit | protein | 104 | 9% helix, 44% strand | Q9WTK5 |
| B | Nuclear factor nf-kappa-B P100 subunit | protein | 103 | 3% helix, 45% strand | Q9WTK5 |
| C | Nuclear factor nf-kappa-B P100 subunit | protein | 102 | 3% helix, 45% strand | Q9WTK5 |
| D | Nuclear factor nf-kappa-B P100 subunit | protein | 102 | 0% helix, 42% strand | Q9WTK5 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.44 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 740 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 595 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3JV5 · Crystal structure of the dimerization domains p52 homodimer · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WTK5 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P100 subunit (Q9WTK5) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9WTK5
- Elsewhere: RCSB PDB 3JV5 · PDBe 3JV5 · UniProt Q9WTK5
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