MolNFT v1 · #146518 · protein
Crystal structure of pparkin (rep and RING2 deleted)-pub-UBCH7 complex
6DJW · Rbr-type E3 ubiquitin TRANSFERASE,RBR-type E3 ubiquitin…: “Crystal structure of pparkin (rep and RING2 deleted)-pub-UBCH7 complex”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.78). MolNFT v1 #146518 on…
- PDB
- 6DJW
- Type
- protein
- Length
- 544 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rbr-type E3 ubiquitin TRANSFERASE,RBR-type E3 ubiquitin transferase; Ubiquitin…
- EC
- 2.3.2.31, 2.3.2.23
- UniProt
- A0A034W4L8, P62992, P68036
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rbr-type E3 ubiquitin TRANSFERASE,RBR-type E3 ubiquitin transferase (EC 2.3.2.31) | protein | 317 | 17% helix, 22% strand | A0A034W4L8 |
| B | Ubiquitin | protein | 74 | 20% helix, 35% strand | P62992 |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 153 | 37% helix, 18% strand | P68036 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.78 | 0.80 | 101 | empty |
| 2 | 69 | 0.73 | 0.96 | 20 | empty |
| 3 | 170 | 0.62 | 0.84 | 31 | empty |
| 4 | 54 | 0.50 | 0.86 | 18 | empty |
| 5 | 158 | 0.46 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1590 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6DJW · Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 A0A034W4L8
- Every structure of UniProt P62992
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 6DJW · PDBe 6DJW · UniProt A0A034W4L8 · UniProt P62992 · UniProt P68036
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