MolNFT v1 · #126070 · protein
Structure of CEZANNE/OTUD7B otu domain bound to ubiquitin
5LRW · Otu domain-containing protein 7B: “Structure of CEZANNE/OTUD7B otu domain bound to ubiquitin”. X-ray diffraction, 1 ligand (NEH), 10 pockets (best druggability 0.71). MolNFT v1 #126070 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LRW
- Type
- protein
- Length
- 706 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Otu domain-containing protein 7B; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q6GQQ9, P0CG47
- Ligands
- NEH
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Otu domain-containing protein 7B (EC 3.4.19.12) | protein | 278 | 42% helix, 18% strand | Q6GQQ9 |
| B, D | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
| C | Otu domain-containing protein 7B (EC 3.4.19.12) | protein | 278 | 42% helix, 18% strand | Q6GQQ9 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.71 | 0.79 | 70 | empty |
| 2 | 391 | 0.66 | 0.80 | 58 | empty |
| 3 | 61 | 0.55 | 0.88 | 18 | empty |
| 4 | 360 | 0.55 | 0.74 | 43 | empty |
| 5 | 127 | 0.54 | 0.82 | 21 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1087 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1073 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5LRW · Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GQQ9 · AlphaFold monomer V2.0 prediction for otu domain-containing protein 7B (Q6GQQ9) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q6GQQ9
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5LRW · PDBe 5LRW · UniProt Q6GQQ9 · UniProt P0CG47
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