Research workbench
USP34 catalytic domain in complex with ubpa
Analyse USP34 catalytic domain in complex with ubpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W3U
- Type
- protein
- Length
- 1,239 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 34; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q70CQ2, J3QS39
- Ligands
- AYE, ZN
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 34 (EC 3.4.19.12) | protein | 343 | 31% helix, 32% strand | Q70CQ2 |
| B | Ubiquitin carboxyl-terminal hydrolase 34 (EC 3.4.19.12) | protein | 338 | 29% helix, 31% strand | Q70CQ2 |
| C | Ubiquitin carboxyl-terminal hydrolase 34 (EC 3.4.19.12) | protein | 333 | 30% helix, 31% strand | Q70CQ2 |
| D, E, F | Polyubiquitin-B | protein | 75 | 20% helix, 32% strand | J3QS39 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 3 copies · chains A, D, B, E, C, F
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.77 | 0.97 | 36 | empty |
| 2 | 109 | 0.77 | 0.96 | 31 | empty |
| 3 | 964 | 0.76 | 0.78 | 86 | empty |
| 4 | 157 | 0.72 | 0.90 | 37 | empty |
| 5 | 296 | 0.67 | 0.82 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–F · 1823 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 1795 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1750 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 985 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7W3U · USP34 catalytic domain in complex with UbPA · the same entry in another collection · chain A against A, TM-score 1.00
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 Q70CQ2
- Every structure of UniProt J3QS39
- Elsewhere: RCSB PDB 7W3U · PDBe 7W3U · UniProt Q70CQ2 · UniProt J3QS39
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