MolNFT v1 · #145173 · protein
Structure of the pr-dub complex
6CGA · Ubiquitin carboxyl-terminal hydrolase calypso: “Structure of the pr-dub complex”. X-ray diffraction, 17 pockets (best druggability 0.62). MolNFT v1 #145173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CGA
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase calypso; Polycomb protein asx
- EC
- 3.4.19.12
- UniProt
- Q7K5N4, Q9V727
- Pockets
- 17 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase calypso (EC 3.4.19.12) | protein | 293 | 41% helix, 10% strand | Q7K5N4 |
| B | Polycomb protein asx | protein | 75 | 49% helix, 1% strand | Q9V727 |
| C | Ubiquitin carboxyl-terminal hydrolase calypso (EC 3.4.19.12) | protein | 284 | 42% helix, 10% strand | Q7K5N4 |
| D | Polycomb protein asx | protein | 76 | 50% helix, 0% strand | Q9V727 |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.62 | 0.92 | 17 | empty |
| 2 | 70 | 0.59 | 0.89 | 16 | empty |
| 3 | 238 | 0.58 | 0.79 | 29 | empty |
| 4 | 191 | 0.57 | 0.80 | 20 | empty |
| 5 | 175 | 0.55 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1465 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1407 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 430 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CGA · Structure of the PR-DUB complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q7K5N4 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase calypso… · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9V727 · AlphaFold monomer V2.0 prediction for polycomb protein asx (Q9V727) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 Q7K5N4
- Every structure of UniProt Q9V727
- Elsewhere: RCSB PDB 6CGA · PDBe 6CGA · UniProt Q7K5N4 · UniProt Q9V727
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