Research workbench
Crystal structure of the uba domain from edd ubiquitin ligase in complex with ubiquitin
Analyse Crystal structure of the uba domain from edd ubiquitin ligase 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
- 2QHO
- Type
- protein
- Length
- 488 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; E3 ubiquitin-protein ligase EDD1
- EC
- 6.3.2.-
- UniProt
- P62990, O95071
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Ubiquitin | protein | 72 | 26% helix, 36% strand | P62990 |
| B | E3 ubiquitin-protein ligase EDD1 (EC 6.3.2.-) | protein | 47 | 68% helix, 0% strand | O95071 |
| C | Ubiquitin | protein | 76 | 24% helix, 34% strand | P62990 |
| D | E3 ubiquitin-protein ligase EDD1 (EC 6.3.2.-) | protein | 49 | 67% helix, 0% strand | O95071 |
| E | Ubiquitin | protein | 75 | 24% helix, 35% strand | P62990 |
| F | E3 ubiquitin-protein ligase EDD1 (EC 6.3.2.-) | protein | 49 | 71% helix, 0% strand | O95071 |
| H | E3 ubiquitin-protein ligase EDD1 (EC 6.3.2.-) | protein | 48 | 69% helix, 0% strand | O95071 |
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 | 510 | 0.65 | 0.77 | 53 | empty |
| 2 | 109 | 0.46 | 0.79 | 22 | empty |
| 3 | 92 | 0.32 | 0.73 | 21 | empty |
Interfaces
11 interfaces between chains.
- E–F · 641 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 563 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 551 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 540 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 326 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2QHO · Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
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 P62990
- Every structure of UniProt O95071
- Elsewhere: RCSB PDB 2QHO · PDBe 2QHO · UniProt P62990 · UniProt O95071
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