Research workbench
USP7CD-UBL45 in complex with ubiquitin
Analyse USP7CD-UBL45 in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JTV
- Type
- protein
- Length
- 2,560 residues
- Chains
- 8
- 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
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 564 | 25% helix, 30% strand | Q93009 |
| B, D, F, H | Polyubiquitin-B | protein | 76 | 21% helix, 33% strand | P0CG47 |
| E | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 565 | 24% helix, 30% strand | Q93009 |
| G | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 563 | 25% helix, 29% strand | Q93009 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.78 | 0.81 | 80 | empty |
| 2 | 845 | 0.77 | 0.80 | 97 | empty |
| 3 | 1107 | 0.77 | 0.79 | 94 | empty |
| 4 | 753 | 0.75 | 0.80 | 56 | empty |
| 5 | 755 | 0.75 | 0.79 | 50 | empty |
Interfaces
17 interfaces between chains.
- A–E · 2372 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 2331 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1850 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 1811 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1794 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5JTV · USP7CD-UBL45 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 5JTV · PDBe 5JTV · UniProt Q93009 · UniProt P0CG47
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