Research workbench
Crystal structure of the mouse HOIL1-L-nzf in complex with linear di- ubiquitin
Analyse Crystal structure of the mouse HOIL1-L-nzf in complex with linear di- ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B0A
- Type
- protein
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C; Ranbp-type and C3HC4-type zinc finger-containing protein 1
- UniProt
- P0CG48, Q9WUB0
- Ligands
- TAM, ZN
- Pockets
- 7 · best druggability 0.37
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyubiquitin-C | protein | 151 | 22% helix, 36% strand | P0CG48 |
| B | Ranbp-type and C3HC4-type zinc finger-containing protein 1 | protein | 57 | 26% helix, 11% strand | Q9WUB0 |
| D | Polyubiquitin-C | protein | 152 | 24% helix, 36% strand | P0CG48 |
| E | Ranbp-type and C3HC4-type zinc finger-containing protein 1 | protein | 63 | 22% helix, 10% strand | Q9WUB0 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.37 | 0.74 | 20 | empty |
| 2 | 81 | 0.33 | 0.74 | 22 | empty |
| 3 | 86 | 0.32 | 0.74 | 20 | empty |
| 4 | 64 | 0.30 | 0.74 | 15 | empty |
| 5 | 68 | 0.29 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- D–E · 957 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 838 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 276 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3B0A · Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WUB0 · AlphaFold monomer V2.0 prediction for ranbp-type and C3HC4-type zinc finger-containing… · a predicted model of the same protein · chain B against A, TM-score 0.81
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 Q9WUB0
- Elsewhere: RCSB PDB 3B0A · PDBe 3B0A · UniProt P0CG48 · UniProt Q9WUB0
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