MolNFT v1 · #89172 · protein
Structure of C. elegans OTUB1 bound to human UBC13
4DHI · Ubiquitin thioesterase otubain-like: “Structure of C. elegans OTUB1 bound to human UBC13”. X-ray diffraction, 4 pockets (best druggability 0.39). MolNFT v1 #89172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DHI
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase otubain-like; Ubiquitin-conjugating enzyme E2 N
- EC
- 3.4.19.12, 6.3.2.19
- UniProt
- Q9XVR6, P61088
- Pockets
- 4 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin thioesterase otubain-like (EC 3.4.19.12) | protein | 238 | 55% helix, 13% strand | Q9XVR6 |
| D | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 150 | 34% helix, 17% strand | P61088 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.39 | 0.75 | 17 | empty |
| 2 | 128 | 0.39 | 0.73 | 23 | empty |
| 3 | 90 | 0.35 | 0.75 | 24 | empty |
| 4 | 56 | 0.28 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- B–D · 664 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4DHI · Structure of C. elegans OTUB1 bound to human UBC13 · the same entry in another collection · chain B against B, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain D against A, TM-score 0.95
- Q9XVR6 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase otubain- like (Q9XVR6) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P61088
- Elsewhere: RCSB PDB 4DHI · PDBe 4DHI · UniProt Q9XVR6 · UniProt P61088
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