MolNFT v1 · #186159 · protein
USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
7R2G · Ubiquitin carboxyl-terminal hydrolase 15: “USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)”. X-ray diffraction, 2 ligands (MIX, ZN), 9 pockets (best druggability 0.56). MolNFT v1 #186159 on…
- PDB
- 7R2G
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15
- EC
- 3.4.19.12
- Ligands
- MIX, ZN
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 346 | 31% helix, 26% strand | — |
| B | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 351 | 31% helix, 26% strand | — |
Ligands and binding sites
- MIX · 1,4-dihydroxy-5,8-bis({2-[(2-hydroxyethyl) amino]ethyl}amino)-9,10-anthracenedione · ligand · 12 copies · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.56 | 0.75 | 46 | empty |
| 2 | 183 | 0.50 | 0.77 | 30 | empty |
| 3 | 173 | 0.46 | 0.75 | 26 | empty |
| 4 | 52 | 0.45 | 0.84 | 18 | empty |
| 5 | 161 | 0.45 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7R2G · USP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2) · 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
- Elsewhere: RCSB PDB 7R2G · PDBe 7R2G
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