MolNFT v1 · #109023 · protein
Crystal structure of USP7 ubiquitin-like domains in extended conformation
4WPI · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 ubiquitin-like domains in extended conformation”. X-ray diffraction, 1 ligand (CL), 9 pockets (best druggability 0.53). MolNFT v1 #109023 on GenesisL1: 3D…
- PDB
- 4WPI
- Type
- protein
- Length
- 701 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
- 9 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 341 | 27% helix, 32% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 340 | 28% helix, 31% strand | Q93009 |
| C, D | ICP0 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.53 | 0.80 | 20 | empty |
| 2 | 294 | 0.52 | 0.74 | 33 | empty |
| 3 | 165 | 0.45 | 0.75 | 28 | empty |
| 4 | 65 | 0.36 | 0.77 | 12 | empty |
| 5 | 117 | 0.35 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 796 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 739 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4WPI · Crystal structure of USP7 ubiquitin-like domains in extended 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 4WPI · PDBe 4WPI · UniProt Q93009
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