Research workbench
Structure of the saga UBP8(S144N)/SGF11/SUS1/SGF73 dub module
Analyse Structure of the saga UBP8(S144N)/SGF11/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
- 4FK5
- Type
- protein
- Length
- 712 residues
- Chains
- 4
- 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
- 10 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 437 | 36% helix, 25% strand | P50102 |
| B | Protein SUS1 | protein | 92 | 79% helix, 3% strand | Q6WNK7 |
| C | Saga-associated factor 11 | protein | 92 | 54% helix, 10% strand | Q03067 |
| E | Saga-associated factor 73 | protein | 91 | 33% helix, 15% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, E
- GOL · Glycerol · additive · 2 copies · chains A, B, C, E
- EDO · 1,2-ethanediol · additive · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.82 | 0.83 | 81 | GOL |
| 2 | 201 | 0.78 | 0.93 | 36 | empty |
| 3 | 175 | 0.57 | 0.81 | 29 | empty |
| 4 | 158 | 0.53 | 0.80 | 28 | empty |
| 5 | 86 | 0.50 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–E · 3261 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2156 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1450 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1241 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 900 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4FK5 · Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module · 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 0.97
- 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 0.96
- 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 0.91
- 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 0.78
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 4FK5 · PDBe 4FK5 · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P53165
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