Research workbench
Structure of ovarian tumor (otu) domain in complex with ubiquitin
Analyse Structure of ovarian tumor (otu) domain in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C0R
- Type
- protein
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase OTU1; Ubiquitin
- EC
- 3.4.19.12
- UniProt
- P43558, P62988
- Ligands
- 3CN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin thioesterase OTU1 (EC 3.4.19.12) | protein | 175 | 37% helix, 20% strand | P43558 |
| B, D | Ubiquitin | protein | 75 | 24% helix, 29% strand | P62988 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.70 | 0.97 | 27 | empty |
| 2 | 102 | 0.69 | 0.92 | 23 | empty |
| 3 | 73 | 0.62 | 0.90 | 18 | empty |
| 4 | 245 | 0.51 | 0.75 | 30 | empty |
| 5 | 229 | 0.50 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1113 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 757 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 3C0R · Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P43558 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTU1 (P43558) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P43558
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3C0R · PDBe 3C0R · UniProt P43558 · UniProt P62988
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