Research workbench
Crystal structure of human OTUB1/UbcH5b~Ub/Ub
Analyse Crystal structure of human OTUB1/UbcH5b~Ub/Ub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DDI
- Type
- protein
- Length
- 1,653 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.802
- Source
- Homo sapiens
- Molecule
- Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1; Polyubiquitin-C
- EC
- 6.3.2.19, 3.4.19.12
- UniProt
- P62837, Q96FW1, P0CG48
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.802 · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 (EC 6.3.2.19, 3.4.19.12) | protein | 399 | 50% helix, 15% strand | P62837, Q96FW1 |
| D, E, F, G, H, I | Polyubiquitin-C | protein | 76 | 22% helix, 34% strand | P0CG48 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.84 | 0.85 | 92 | empty |
| 2 | 1147 | 0.84 | 0.85 | 108 | empty |
| 3 | 1031 | 0.83 | 0.85 | 96 | empty |
| 4 | 132 | 0.57 | 0.83 | 21 | empty |
| 5 | 135 | 0.56 | 0.82 | 20 | empty |
Interfaces
15 interfaces between chains.
- A–D · 1255 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1253 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1242 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1202 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1184 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4DDI · Crystal structure of human OTUB1/UBCH5B~UB/UB · the same entry in another collection · chain I against I, TM-score 1.00
- P0CG48 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CG48) · a predicted model of the same protein · chain D against A, TM-score 0.91
- Q96FW1 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTUB1 (Q96FW1) · a predicted model of the same protein · chain A against A, TM-score 0.63
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.36
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 P62837
- Every structure of UniProt Q96FW1
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4DDI · PDBe 4DDI · UniProt P62837 · UniProt Q96FW1 · UniProt P0CG48
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