Research workbench
Structure of the saga UBP8/SGF11(1-72, delta-ZNF)/SUS1/SGF73 dub module
Analyse Structure of the saga UBP8/SGF11(1-72, delta-ZNF)/SUS1/SGF73 dub module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FJC
- Type
- protein
- Length
- 1,311 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 8; Protein SUS1; Saga-associated factor 11…
- EC
- 3.4.19.12
- UniProt
- P50102, Q6WNK7, Q03067, P53165
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 447 | 33% helix, 26% strand | P50102 |
| B | Protein SUS1 | protein | 92 | 80% helix, 3% strand | Q6WNK7 |
| C | Saga-associated factor 11 | protein | 43 | 79% helix, 2% strand | Q03067 |
| D | Saga-associated factor 73 | protein | 90 | 33% helix, 17% strand | P53165 |
| E | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 434 | 32% helix, 28% strand | P50102 |
| F | Protein SUS1 | protein | 87 | 85% helix, 0% strand | Q6WNK7 |
| G | Saga-associated factor 11 | protein | 41 | 83% helix, 0% strand | Q03067 |
| H | Saga-associated factor 73 | protein | 77 | 35% helix, 12% strand | P53165 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.85 | 0.86 | 99 | GOL |
| 2 | 1181 | 0.84 | 0.85 | 96 | empty |
| 3 | 196 | 0.56 | 0.79 | 28 | empty |
| 4 | 69 | 0.48 | 0.84 | 19 | empty |
| 5 | 186 | 0.48 | 0.76 | 25 | empty |
Interfaces
19 interfaces between chains.
- A–E · 2034 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 1675 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1668 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1593 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 1532 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4FJC · Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module · the same entry in another collection · chain H against H, TM-score 1.00
- Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain F against A, TM-score 0.95
- Q03067 · AlphaFold monomer V2.0 prediction for saga-associated factor 11 (Q03067) · a predicted model of the same protein · chain G against A, TM-score 0.93
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 Q6WNK7
- Every structure of UniProt Q03067
- Every structure of UniProt P53165
- Elsewhere: RCSB PDB 4FJC · PDBe 4FJC · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P53165
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