Research workbench
Structure of hoip pub domain bound to otulin pim
Analyse Structure of hoip pub domain bound to otulin pim in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OYK
- Type
- protein
- Length
- 374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Ubiquitin thioesterase otulin
- EC
- 6.3.2.-, 3.4.19.12
- UniProt
- Q96EP0, Q96BN8
- Ligands
- CL
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 173 | 58% helix, 5% strand | Q96EP0 |
| B | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 173 | 58% helix, 5% strand | Q96EP0 |
| C | Ubiquitin thioesterase otulin (EC 3.4.19.12) | protein | 13 | 38% helix, 0% strand | Q96BN8 |
| D | Ubiquitin thioesterase otulin (EC 3.4.19.12) | protein | 15 | 53% helix, 0% strand | Q96BN8 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.73 | 0.80 | 70 | empty |
| 2 | 106 | 0.52 | 0.82 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 734 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 526 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4OYK · Structure of HOIP PUB domain bound to OTULIN PIM · the same entry in another collection · chain D against D, TM-score 1.00
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q96BN8 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase otulin (Q96BN8) · a predicted model of the same protein · chain D against A, TM-score 0.51
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 Q96EP0
- Every structure of UniProt Q96BN8
- Elsewhere: RCSB PDB 4OYK · PDBe 4OYK · UniProt Q96EP0 · UniProt Q96BN8
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