Research workbench
The structure of the A20-binding inhibitor of nf-kb 1 in complex with di-ubiquitin
Analyse The structure of the A20-binding inhibitor of nf-kb 1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EAL
- Type
- protein
- Length
- 558 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; TNFAIP3-interacting protein 1
- UniProt
- P0CG48, Q15025
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin | protein | 152 | 22% helix, 34% strand | P0CG48 |
| B | TNFAIP3-interacting protein 1 | protein | 62 | 90% helix, 0% strand | Q15025 |
| C | TNFAIP3-interacting protein 1 | protein | 61 | 90% helix, 0% strand | Q15025 |
| E | TNFAIP3-interacting protein 1 | protein | 65 | 94% helix, 0% strand | Q15025 |
| F | TNFAIP3-interacting protein 1 | protein | 66 | 95% helix, 0% strand | Q15025 |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.60 | 0.75 | 41 | empty |
| 2 | 119 | 0.36 | 0.73 | 14 | empty |
| 3 | 54 | 0.30 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1854 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1788 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 889 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 799 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 523 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7EAL · The structure of the A20-Binding Inhibitor of NF-kB 1 in complex with di-ubiquitin · the same entry in another collection · chain F against F, TM-score 1.00
- Q15025 · AlphaFold monomer V2.0 prediction for TNFAIP3-interacting protein 1 (Q15025) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P0CG48
- Every structure of UniProt Q15025
- Elsewhere: RCSB PDB 7EAL · PDBe 7EAL · UniProt P0CG48 · UniProt Q15025
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