Research workbench
The structure of H/CEOTUB1-ubiquitin aldehyde-UBCH5B~UB
Analyse The structure of H/CEOTUB1-ubiquitin aldehyde-UBCH5B~UB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LDT
- Type
- protein
- Length
- 555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase otubain-like; Ubiquitin aldehyde; Ubiquitin-conjugating enzyme E2…
- EC
- 3.4.19.12, 6.3.2.19
- UniProt
- Q96FW1, Q9XVR6, P0CG48, P62837
- Ligands
- MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 255 | 58% helix, 13% strand | Q96FW1, Q9XVR6 |
| B | Ubiquitin aldehyde | protein | 76 | 20% helix, 36% strand | P0CG48 |
| C | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 148 | 37% helix, 18% strand | P62837 |
| D | Ubiquitin | protein | 76 | 24% helix, 33% strand | P0CG48 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.77 | 0.80 | 97 | EDO |
| 2 | 263 | 0.57 | 0.78 | 29 | empty |
| 3 | 138 | 0.51 | 0.80 | 22 | empty |
| 4 | 62 | 0.40 | 0.81 | 20 | empty |
| 5 | 89 | 0.36 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1120 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1110 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1062 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 235 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 204 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4LDT · The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub · the same entry in another collection · chain B against B, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 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 0.96
- Q96FW1 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTUB1 (Q96FW1) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P62837
- Elsewhere: RCSB PDB 4LDT · PDBe 4LDT · UniProt Q96FW1 · UniProt Q9XVR6 · UniProt P0CG48 · UniProt P62837
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