Research workbench
Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module
Analyse Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M99
- Type
- protein
- Length
- 686 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Saccharomyces cerevisiae
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 8; SAGA-associated factor 11; Protein SUS1…
- EC
- 3.1.2.15
- UniProt
- P50102, Q03067, Q6WNK7, P53165
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.7 · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 422 | 32% helix, 25% strand | P50102 |
| B | SAGA-associated factor 11 | protein | 89 | 48% helix, 7% strand | Q03067 |
| C | Protein SUS1 | protein | 91 | 74% helix, 1% strand | Q6WNK7 |
| D | SAGA-associated factor 73 | protein | 84 | 33% helix, 8% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.83 | 0.84 | 95 | empty |
| 2 | 274 | 0.59 | 0.78 | 27 | empty |
| 3 | 168 | 0.54 | 0.80 | 28 | empty |
| 4 | 168 | 0.53 | 0.79 | 19 | empty |
| 5 | 65 | 0.48 | 0.85 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3156 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2093 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1388 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 1244 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 760 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3M99 · Structure of the UBP8-SGF11-SGF73-SUS1 saga dub module · the same entry in another collection · chain D against D, TM-score 1.00
- P50102 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 8 (P50102) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain C against A, TM-score 0.91
- P53165 · AlphaFold monomer V2.0 prediction for saga-associated factor 73 (P53165) · a predicted model of the same protein · chain D against A, TM-score 0.90
- Q03067 · AlphaFold monomer V2.0 prediction for saga-associated factor 11 (Q03067) · a predicted model of the same protein · chain B against A, TM-score 0.69
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 P50102
- Every structure of UniProt Q03067
- Every structure of UniProt Q6WNK7
- Every structure of UniProt P53165
- Elsewhere: RCSB PDB 3M99 · PDBe 3M99 · UniProt P50102 · UniProt Q03067 · UniProt Q6WNK7 · UniProt P53165
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