MolNFT v1 · #87040 · protein
Structure of OTUD2 otu domain in complex with ubiquitin K11-linked peptide
4BOS · Ubiquitin thioesterase OTU1: “Structure of OTUD2 otu domain in complex with ubiquitin K11-linked peptide”. X-ray diffraction, 2 ligands (MG, NO3), 5 pockets (best druggability 0.72). MolNFT v1 #87040 on GenesisL1: 3D structure…
- PDB
- 4BOS
- Type
- protein
- Length
- 485 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase OTU1; Polyubiquitin-C; OTUD2
- EC
- 3.4.19.12
- UniProt
- Q5VVQ6, P0CG48
- Ligands
- MG, NO3
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin thioesterase OTU1 (EC 3.4.19.12) | protein | 164 | 41% helix, 20% strand | Q5VVQ6 |
| C | Polyubiquitin-C | protein | 76 | 20% helix, 34% strand | P0CG48 |
| E | Polyubiquitin-C | protein | 74 | 19% helix, 32% strand | P0CG48 |
| F | OTUD2 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.72 | 0.95 | 24 | empty |
| 2 | 604 | 0.68 | 0.77 | 75 | NO3 |
| 3 | 276 | 0.67 | 0.83 | 42 | NO3 |
| 4 | 59 | 0.35 | 0.78 | 20 | empty |
| 5 | 87 | 0.35 | 0.75 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1024 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 605 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 266 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 4BOS · Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide · the same entry in another collection · chain A against A, 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 0.98
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 4BOS · PDBe 4BOS · UniProt Q5VVQ6 · UniProt P0CG48
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