Research workbench
Crystal structure of otulin otu domain (C129A) in complex with MET1-di ubiquitin
Analyse Crystal structure of otulin otu domain (C129A) in complex with MET1-di ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZNZ
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FAM105B; Polyubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q96BN8, F5H265
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FAM105B (EC 3.4.19.12) | protein | 266 | 55% helix, 12% strand | Q96BN8 |
| B | Polyubiquitin-C | protein | 146 | 25% helix, 31% strand | F5H265 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.58 | 0.79 | 39 | SO4 |
| 2 | 54 | 0.56 | 0.90 | 16 | empty |
| 3 | 61 | 0.33 | 0.76 | 15 | empty |
| 4 | 61 | 0.30 | 0.76 | 17 | empty |
| 5 | 51 | 0.28 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1927 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3ZNZ · Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q96BN8 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase otulin (Q96BN8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q96BN8
- Every structure of UniProt F5H265
- Elsewhere: RCSB PDB 3ZNZ · PDBe 3ZNZ · UniProt Q96BN8 · UniProt F5H265
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