Research workbench
Crystal structure of the catalytic domain of human USP9X
Analyse Crystal structure of the catalytic domain of human USP9X in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WCH
- Type
- protein
- Length
- 1,353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ubiquitin carboxyl-terminal hydrolase faf-X
- EC
- 3.4.19.12
- UniProt
- Q93008
- Ligands
- ZN, UNX
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ubiquitin carboxyl-terminal hydrolase faf-X (EC 3.4.19.12) | protein | 350 | 31% helix, 34% strand | Q93008 |
| B | Probable ubiquitin carboxyl-terminal hydrolase faf-X (EC 3.4.19.12) | protein | 331 | 31% helix, 35% strand | Q93008 |
| C | Probable ubiquitin carboxyl-terminal hydrolase faf-X (EC 3.4.19.12) | protein | 342 | 31% helix, 34% strand | Q93008 |
| D | Probable ubiquitin carboxyl-terminal hydrolase faf-X (EC 3.4.19.12) | protein | 330 | 31% helix, 36% strand | Q93008 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.69 | 0.75 | 78 | empty |
| 2 | 450 | 0.65 | 0.78 | 49 | empty |
| 3 | 376 | 0.54 | 0.73 | 50 | empty |
| 4 | 240 | 0.53 | 0.77 | 31 | empty |
| 5 | 224 | 0.53 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 848 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 832 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 225 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 212 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 132 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WCH · Crystal structure of the catalytic domain of human USP9X · 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 Q93008
- Elsewhere: RCSB PDB 5WCH · PDBe 5WCH · UniProt Q93008
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