MolNFT v1 · #140977 · protein
Sdea mart-C domain wt apo
5YSJ · UBIQUITINATING/DEUBIQUITINATING enzyme sdea: “Sdea mart-C domain wt apo”. X-ray diffraction, 8 pockets (best druggability 0.73). MolNFT v1 #140977 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YSJ
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBIQUITINATING/DEUBIQUITINATING enzyme sdea
- EC
- 3.4.22.-
- UniProt
- Q5ZTK4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-) | protein | 138 | 30% helix, 33% strand | Q5ZTK4 |
| B | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-) | protein | 140 | 28% helix, 35% strand | Q5ZTK4 |
| C | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-) | protein | 138 | 28% helix, 33% strand | Q5ZTK4 |
| D | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-) | protein | 144 | 29% helix, 32% strand | Q5ZTK4 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.73 | 0.79 | 75 | empty |
| 2 | 180 | 0.57 | 0.81 | 24 | empty |
| 3 | 112 | 0.46 | 0.79 | 19 | empty |
| 4 | 128 | 0.45 | 0.77 | 19 | empty |
| 5 | 126 | 0.43 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1077 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1066 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 355 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 235 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q5ZTK4
- Elsewhere: RCSB PDB 5YSJ · PDBe 5YSJ · UniProt Q5ZTK4
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