MolNFT v1 · #71549 · protein
Structure of the saga UBP8/SGF11/SUS1/SGF73 dub module
3MHH · Ubiquitin carboxyl-terminal hydrolase 8: “Structure of the saga UBP8/SGF11/SUS1/SGF73 dub module”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.82). MolNFT v1 #71549 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3MHH
- Type
- protein
- Length
- 711 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
- 3.1.2.15
- UniProt
- P50102, Q6WNK7, Q03067, P53165
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 433 | 36% helix, 25% strand | P50102 |
| B | Protein SUS1 | protein | 93 | 78% helix, 3% strand | Q6WNK7 |
| C | Saga-associated factor 11 | protein | 93 | 52% helix, 8% strand | Q03067 |
| E | Saga-associated factor 73 | protein | 92 | 35% helix, 15% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.82 | 0.83 | 78 | empty |
| 2 | 89 | 0.72 | 0.95 | 16 | empty |
| 3 | 186 | 0.65 | 0.85 | 43 | empty |
| 4 | 156 | 0.55 | 0.81 | 27 | empty |
| 5 | 87 | 0.50 | 0.83 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–E · 3191 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 2151 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1434 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 845 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3MHH · Structure of the SAGA Ubp8/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 3MHH · PDBe 3MHH · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P53165
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