Research workbench
Structure of the saga UBP8/SGF11/SUS1/SGF73 dub module bound to ubiquitin aldehyde
Analyse Structure of the saga UBP8/SGF11/SUS1/SGF73 dub module bound to ubiquitin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MHS
- Type
- protein
- Length
- 801 residues
- Chains
- 5
- 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
- 3.1.2.15
- UniProt
- P50102, Q6WNK7, Q03067, P62988, P53165
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 455 | 34% helix, 26% strand | P50102 |
| B | Protein SUS1 | protein | 91 | 82% helix, 2% strand | Q6WNK7 |
| C | Saga-associated factor 11 | protein | 93 | 48% helix, 8% strand | Q03067 |
| D | Ubiquitin | protein | 76 | 24% helix, 33% strand | P62988 |
| E | Saga-associated factor 73 | protein | 86 | 30% helix, 12% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, E
- EDO · 1,2-ethanediol · additive · chains A, D
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.82 | 0.83 | 73 | empty |
| 2 | 233 | 0.80 | 0.93 | 52 | empty |
| 3 | 158 | 0.57 | 0.82 | 27 | empty |
| 4 | 89 | 0.49 | 0.82 | 17 | empty |
| 5 | 179 | 0.47 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–E · 3313 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 2159 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1785 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1433 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1263 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3MHS · Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde · the same entry in another collection · chain E against E, 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 0.99
- P53165 · AlphaFold monomer V2.0 prediction for saga-associated factor 73 (P53165) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q6WNK7 · AlphaFold monomer V2.0 prediction for transcription and mRNA export factor SUS1 (Q6WNK7) · a predicted model of the same protein · chain B against A, TM-score 0.93
- Q03067 · AlphaFold monomer V2.0 prediction for saga-associated factor 11 (Q03067) · a predicted model of the same protein · chain C against A, TM-score 0.74
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 P62988
- Every structure of UniProt P53165
- Elsewhere: RCSB PDB 3MHS · PDBe 3MHS · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P62988 · UniProt P53165
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.