Research workbench
The structure of H/CEOTUB1-ubiquitin aldehyde-UBC13~UB
Analyse The structure of H/CEOTUB1-ubiquitin aldehyde-UBC13~UB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DHZ
- Type
- protein
- Length
- 553 residues
- Chains
- 4
- 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
- Q96FW1, Q9XVR6, P0CG48, P61088
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 256 | 56% helix, 13% strand | Q96FW1, Q9XVR6 |
| B | Ubiquitin aldehyde | protein | 76 | 24% helix, 37% strand | P0CG48 |
| E | Ubiquitin | protein | 72 | 18% helix, 32% strand | P0CG48 |
| F | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 149 | 32% helix, 20% strand | P61088 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.76 | 0.79 | 77 | empty |
| 2 | 224 | 0.56 | 0.79 | 34 | empty |
| 3 | 272 | 0.56 | 0.77 | 28 | empty |
| 4 | 90 | 0.50 | 0.82 | 20 | empty |
| 5 | 152 | 0.49 | 0.78 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1215 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 841 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 779 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 97 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 16 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4DHZ · The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XVR6 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase otubain- like (Q9XVR6) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain F against A, TM-score 0.95
- Q96FW1 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTUB1 (Q96FW1) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q96FW1
- Every structure of UniProt Q9XVR6
- Every structure of UniProt P0CG48
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 4DHZ · PDBe 4DHZ · UniProt Q96FW1 · UniProt Q9XVR6 · UniProt P0CG48 · UniProt P61088
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