Research workbench
The structure of a CEOTUB1 ubiquitin aldehyde UBC13~UB complex
Analyse The structure of a CEOTUB1 ubiquitin aldehyde UBC13~UB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DHJ
- Type
- protein
- Length
- 2,014 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase otubain-like; Ubiquitin aldehyde; Ubiquitin; Ubiquitin-conjugating…
- EC
- 3.4.19.12, 6.3.2.19
- UniProt
- Q9XVR6, P0CG48, P61088
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 248 | 54% helix, 13% strand | Q9XVR6 |
| B, F, J, M | Ubiquitin aldehyde | protein | 76 | 24% helix, 36% strand | P0CG48 |
| E | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 245 | 53% helix, 14% strand | Q9XVR6 |
| D, H | Ubiquitin | protein | 71 | 17% helix, 32% strand | P0CG48 |
| C | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 149 | 34% helix, 19% strand | P61088 |
| I | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 241 | 53% helix, 15% strand | Q9XVR6 |
| K, G | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 148 | 34% helix, 18% strand | P61088 |
| L | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 239 | 52% helix, 14% strand | Q9XVR6 |
| N | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 150 | 34% helix, 21% strand | P61088 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.76 | 0.80 | 77 | empty |
| 2 | 315 | 0.63 | 0.79 | 27 | empty |
| 3 | 371 | 0.61 | 0.77 | 28 | empty |
| 4 | 336 | 0.58 | 0.77 | 51 | empty |
| 5 | 325 | 0.58 | 0.77 | 33 | empty |
Interfaces
19 interfaces between chains.
- L–M · 1167 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1167 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1161 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1159 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 812 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4DHJ · The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex · the same entry in another collection · chain N against N, 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 Q9XVR6
- Every structure of UniProt P0CG48
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 4DHJ · PDBe 4DHJ · UniProt Q9XVR6 · UniProt P0CG48 · UniProt P61088
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