MolNFT v1 · #87045 · protein
Structure of OTUD2 otu domain in complex with K11-linked di ubiquitin
4BOZ · Ubiquitin thioesterase OTU1: “Structure of OTUD2 otu domain in complex with K11-linked di ubiquitin”. X-ray diffraction, 6 pockets (best druggability 0.61). MolNFT v1 #87045 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4BOZ
- Type
- protein
- Length
- 546 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase OTU1; Ubiquitin-C
- EC
- 3.4.19.12
- UniProt
- Q5VVQ6, P0CG48
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase OTU1 (EC 3.4.19.12) | protein | 158 | 39% helix, 21% strand | Q5VVQ6 |
| B, E | Ubiquitin-C | protein | 76 | 16% helix, 28% strand | P0CG48 |
| C | Ubiquitin-C | protein | 71 | 24% helix, 34% strand | P0CG48 |
| D | Ubiquitin thioesterase OTU1 (EC 3.4.19.12) | protein | 165 | 42% helix, 20% strand | Q5VVQ6 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.61 | 0.77 | 48 | empty |
| 2 | 114 | 0.60 | 0.86 | 32 | empty |
| 3 | 156 | 0.52 | 0.79 | 21 | empty |
| 4 | 150 | 0.44 | 0.75 | 28 | empty |
| 5 | 116 | 0.42 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 993 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 973 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 254 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4BOZ · Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin · the same entry in another collection · chain E against E, TM-score 1.00
- Q5VVQ6 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTU1 (Q5VVQ6) · 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 Q5VVQ6
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4BOZ · PDBe 4BOZ · UniProt Q5VVQ6 · UniProt P0CG48
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