MolNFT v1 · #54993 · protein
Structure of the D1D2 domain of USP4, the conserved catalytic domain
2Y6E · Ubiquitin carboxyl-terminal hydrolase 4: “Structure of the D1D2 domain of USP4, the conserved catalytic domain”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #54993 on GenesisL1: 3D…
- PDB
- 2Y6E
- Type
- protein
- Length
- 1,977 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 4
- EC
- 3.1.2.15
- UniProt
- Q13107
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 337 | 29% helix, 28% strand | Q13107 |
| B | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 339 | 30% helix, 28% strand | Q13107 |
| C | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 331 | 30% helix, 28% strand | Q13107 |
| D | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 328 | 30% helix, 27% strand | Q13107 |
| E | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 319 | 31% helix, 28% strand | Q13107 |
| F | Ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) | protein | 323 | 30% helix, 28% strand | Q13107 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.78 | 0.81 | 94 | empty |
| 2 | 607 | 0.77 | 0.83 | 69 | empty |
| 3 | 571 | 0.70 | 0.79 | 54 | empty |
| 4 | 282 | 0.69 | 0.84 | 42 | empty |
| 5 | 570 | 0.69 | 0.78 | 65 | empty |
Interfaces
12 interfaces between chains.
- E–F · 572 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 510 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 477 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 430 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 361 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 2Y6E · Structure of the D1D2 domain of USP4, the conserved catalytic domain · the same entry in another collection · chain F against F, TM-score 1.00
- Q13107 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 4 (Q13107) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q13107
- Elsewhere: RCSB PDB 2Y6E · PDBe 2Y6E · UniProt Q13107
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