MolNFT v1 · #115143 · protein
Structure of pediculus humanus parkin bound to phospho-ubiquitin
5CAW · E3 ubiquitin-protein ligase parkin: “Structure of pediculus humanus parkin bound to phospho-ubiquitin”. X-ray diffraction, 3 ligands (3CN, ZN, SO4), 5 pockets (best druggability 0.66). MolNFT v1 #115143 on GenesisL1: 3D structure…
- PDB
- 5CAW
- Type
- protein
- Length
- 763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase parkin; Polyubiquitin-B
- EC
- 6.3.2.-
- UniProt
- E0VIU9, P0CG47
- Ligands
- 3CN, ZN, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 298 | 18% helix, 25% strand | E0VIU9 |
| B, D | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | P0CG47 |
| C | E3 ubiquitin-protein ligase parkin (EC 6.3.2.-) | protein | 315 | 17% helix, 24% strand | E0VIU9 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 16 copies · chains A, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.66 | 0.76 | 68 | SO4 |
| 2 | 535 | 0.65 | 0.76 | 67 | SO4 |
| 3 | 60 | 0.39 | 0.80 | 16 | SO4 |
| 4 | 59 | 0.36 | 0.78 | 15 | empty |
| 5 | 64 | 0.34 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1177 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1164 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 5CAW · Structure of Pediculus humanus Parkin bound to phospho-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 E0VIU9
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5CAW · PDBe 5CAW · UniProt E0VIU9 · UniProt P0CG47
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