Research workbench
Structure of the USP15 deubiquitinase domain in complex with an affinity-matured inhibitory ubv
Analyse Structure of the USP15 deubiquitinase domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ML1
- Type
- protein
- Length
- 812 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15,UBIQUITIN carboxyl-terminal hydrolase…
- EC
- 3.4.19.12
- UniProt
- Q9Y4E8, A0A0L7RG06
- Ligands
- CA, NA, ZN, CL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 15,UBIQUITIN carboxyl-terminal hydrolase 15,UBIQUITIN carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 316 | 28% helix, 29% strand | Q9Y4E8 |
| B | Ubiquitin carboxyl-terminal hydrolase 15,UBIQUITIN carboxyl-terminal hydrolase 15,UBIQUITIN carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 321 | 28% helix, 29% strand | Q9Y4E8 |
| E | Ubiquitin variant 15.1A | protein | 83 | 22% helix, 35% strand | A0A0L7RG06 |
| C | Ubiquitin variant 15.1A | protein | 87 | 22% helix, 36% strand | A0A0L7RG06 |
| G | Proteolyzed N-terminal tag of UBV.15.1A construct | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, G, C
- NA · Sodium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.80 | 0.81 | 82 | empty |
| 2 | 940 | 0.79 | 0.81 | 60 | empty |
| 3 | 627 | 0.68 | 0.77 | 41 | CL |
| 4 | 137 | 0.53 | 0.81 | 18 | empty |
| 5 | 147 | 0.51 | 0.79 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1147 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1073 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 385 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 297 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6ML1 · Structure of the USP15 deubiquitinase domain in complex with an affinity-matured… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y4E8 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 15 (Q9Y4E8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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
- Every structure of UniProt A0A0L7RG06
- Elsewhere: RCSB PDB 6ML1 · PDBe 6ML1 · UniProt Q9Y4E8 · UniProt A0A0L7RG06
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