Research workbench
Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin
Analyse Crystal structure of USP7 catalytic domain [H294E] mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KYE
- Type
- protein
- Length
- 825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q93009, P0CG47
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 343 | 34% helix, 29% strand | Q93009 |
| D, C | Polyubiquitin-B | protein | 76 | 24% helix, 30% strand | P0CG47 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 330 | 33% helix, 30% strand | Q93009 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.75 | 0.85 | 54 | empty |
| 2 | 1119 | 0.74 | 0.77 | 95 | empty |
| 3 | 83 | 0.36 | 0.76 | 12 | empty |
| 4 | 54 | 0.35 | 0.79 | 16 | empty |
| 5 | 78 | 0.33 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1896 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1822 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 693 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KYE · Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin · 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 Q93009
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5KYE · PDBe 5KYE · UniProt Q93009 · UniProt P0CG47
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