MolNFT v1 · #109022 · protein
Crystal structure of USP7 ubiquitin-like domains in compact conformation
4WPH · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 ubiquitin-like domains in compact conformation”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.75). MolNFT v1 #109022 on GenesisL1: 3D…
- PDB
- 4WPH
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; ICP0
- EC
- 3.4.19.12
- UniProt
- Q93009
- Ligands
- CL
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 337 | 28% helix, 32% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 326 | 29% helix, 33% strand | Q93009 |
| C | ICP0 | protein | 10 | 0% helix, 0% strand | — |
| D | ICP0 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.75 | 0.81 | 75 | empty |
| 2 | 220 | 0.67 | 0.85 | 39 | empty |
| 3 | 336 | 0.60 | 0.78 | 29 | empty |
| 4 | 99 | 0.48 | 0.81 | 18 | empty |
| 5 | 141 | 0.44 | 0.76 | 29 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1235 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 723 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 659 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 52 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4WPH · Crystal structure of USP7 ubiquitin-like domains in compact conformation · 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
- Elsewhere: RCSB PDB 4WPH · PDBe 4WPH · UniProt Q93009
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