Research workbench
Yeast deubiquitinase UBP3 and BRE5 cofactor complex
Analyse Yeast deubiquitinase UBP3 and BRE5 cofactor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QIY
- Type
- protein
- Length
- 317 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBP3-associated protein BRE5; Ubiquitin carboxyl-terminal hydrolase 3
- EC
- 3.1.2.15
- UniProt
- P53741, Q01477
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UBP3-associated protein BRE5 | protein | 134 | 31% helix, 46% strand | P53741 |
| C, D | Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) | protein | 25 | 60% helix, 12% strand | Q01477 |
| B | UBP3-associated protein BRE5 | protein | 133 | 30% helix, 47% strand | P53741 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.46 | 0.80 | 27 | empty |
| 2 | 67 | 0.34 | 0.76 | 11 | empty |
| 3 | 63 | 0.34 | 0.77 | 14 | empty |
| 4 | 57 | 0.30 | 0.75 | 13 | empty |
| 5 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1394 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 924 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 822 Ų buried · 12 hydrogen bonds · protein-protein
- C–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2QIY · yeast Deubiquitinase Ubp3 and Bre5 cofactor complex · the same entry in another collection · chain A against A, TM-score 1.00
- P53741 · AlphaFold monomer V2.0 prediction for UBP3-associated protein BRE5 (P53741) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q01477 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 3 (Q01477) · a predicted model of the same protein · chain C against A, TM-score 0.61
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 P53741
- Every structure of UniProt Q01477
- Elsewhere: RCSB PDB 2QIY · PDBe 2QIY · UniProt P53741 · UniProt Q01477
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