Research workbench
UbcH5c~Ubiquitin Conjugate
Analyse UbcH5c~Ubiquitin Conjugate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UGB
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Homo sapiens
- Molecule
- Ubiquitin-conjugating enzyme E2 D3; Polyubiquitin-C
- EC
- 6.3.2.19
- UniProt
- P61077, P0CG48
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) | protein | 146 | 37% helix, 18% strand | P61077 |
| B | Polyubiquitin-C | protein | 76 | 20% helix, 30% strand | P0CG48 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.56 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UGB · UBCH5C~UBIQUITIN conjugate · the same entry in another collection · chain A against A, TM-score 1.00
- P61077 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D3 (P61077) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0CG48 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG48) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P61077
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 3UGB · PDBe 3UGB · UniProt P61077 · UniProt P0CG48
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