Research workbench
Crystal structure of the U-box domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme
Analyse Crystal structure of the U-box domain of human E4B ubiquitin ligase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L1Z
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D3; Ubiquitin conjugation factor E4 B
- EC
- 6.3.2.19
- UniProt
- P61077, O95155
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) | protein | 152 | 36% helix, 16% strand | P61077 |
| B | Ubiquitin conjugation factor E4 B | protein | 78 | 37% helix, 15% strand | O95155 |
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 | 355 | 0.61 | 0.78 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 550 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3L1Z · Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with… · 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 0.96
- O95155 · AlphaFold monomer V2.0 prediction for ubiquitin conjugation factor E4 B (O95155) · 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 O95155
- Elsewhere: RCSB PDB 3L1Z · PDBe 3L1Z · UniProt P61077 · UniProt O95155
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