MolNFT v1 · #143140 · protein
Saga dub module UBP8(C146A)/SGF11/SUS1/SGF73 bound to monoubiquitin
6AQR · Ubiquitin carboxyl-terminal hydrolase 8: “Saga dub module UBP8(C146A)/SGF11/SUS1/SGF73 bound to monoubiquitin”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.85). MolNFT v1 #143140 on GenesisL1: 3D structure…
- PDB
- 6AQR
- Type
- protein
- Length
- 784 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 8; Transcription and mRNA export factor SUS1…
- EC
- 3.4.19.12
- UniProt
- P50102, Q6WNK7, Q03067, P0CG48, P53165
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.4.19.12) | protein | 442 | 35% helix, 26% strand | P50102 |
| B | Transcription and mRNA export factor SUS1 | protein | 91 | 81% helix, 2% strand | Q6WNK7 |
| C | Saga-associated factor 11 | protein | 87 | 52% helix, 7% strand | Q03067 |
| D | Polyubiquitin-C | protein | 76 | 25% helix, 33% strand | P0CG48 |
| E | Saga-associated factor 73 | protein | 88 | 34% helix, 13% strand | P53165 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.85 | 0.86 | 118 | empty |
| 2 | 173 | 0.57 | 0.82 | 27 | empty |
| 3 | 100 | 0.49 | 0.81 | 22 | empty |
| 4 | 111 | 0.46 | 0.79 | 20 | empty |
| 5 | 72 | 0.44 | 0.81 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–E · 3230 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 2130 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1828 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1356 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1286 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6AQR · SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin · 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 0.80
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 P0CG48
- Every structure of UniProt P53165
- Elsewhere: RCSB PDB 6AQR · PDBe 6AQR · UniProt P50102 · UniProt Q6WNK7 · UniProt Q03067 · UniProt P0CG48 · UniProt P53165
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.