MolNFT v1 · #146495 · protein
Structure of the USP15 dusp domain in complex with a high-affinity ubiquitin variant (ubv)
6DJ9 · Ubiquitin carboxyl-terminal hydrolase 15: “Structure of the USP15 dusp domain in complex with a high-affinity ubiquitin variant (ubv)”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #146495 on GenesisL1: 3D…
- PDB
- 6DJ9
- Type
- protein
- Length
- 1,221 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15; Ubiquitin variant ubv 15.D
- EC
- 3.4.19.12
- UniProt
- Q9Y4E8
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 25% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 131 | 23% helix, 13% strand | Q9Y4E8 |
| B | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 123 | 30% helix, 11% strand | Q9Y4E8 |
| C | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 123 | 26% helix, 13% strand | Q9Y4E8 |
| D | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 122 | 28% helix, 13% strand | Q9Y4E8 |
| E | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 126 | 23% helix, 13% strand | Q9Y4E8 |
| F | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 131 | 31% helix, 13% strand | Q9Y4E8 |
| G, K | Ubiquitin variant ubv 15.D | protein | 77 | 17% helix, 23% strand | — |
| H, I, L | Ubiquitin variant ubv 15.D | protein | 78 | 19% helix, 14% strand | — |
| J | Ubiquitin variant ubv 15.D | protein | 77 | 25% helix, 30% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.79 | 0.81 | 106 | empty |
| 2 | 123 | 0.76 | 0.95 | 27 | empty |
| 3 | 1027 | 0.73 | 0.76 | 77 | empty |
| 4 | 601 | 0.71 | 0.79 | 62 | empty |
| 5 | 400 | 0.69 | 0.81 | 51 | empty |
Interfaces
27 interfaces between chains.
- G–L · 2043 Ų buried · 37 hydrogen bonds · protein-protein
- I–J · 2004 Ų buried · 31 hydrogen bonds · protein-protein
- D–H · 622 Ų buried · 10 hydrogen bonds · protein-protein
- A–K · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6DJ9 · Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV) · the same entry in another collection · chain L against L, 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 Q9Y4E8
- Elsewhere: RCSB PDB 6DJ9 · PDBe 6DJ9 · UniProt Q9Y4E8
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