MolNFT v1 · #146519 · protein
Crystal structure of pparkin-pub-UBCH7 complex
6DJX · Rbr-type E3 ubiquitin TRANSFERASE,RBR-type E3 ubiquitin…: “Crystal structure of pparkin-pub-UBCH7 complex”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.78). MolNFT v1 #146519 on GenesisL1: 3D structure, binding…
- PDB
- 6DJX
- 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
- 7 · 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, 36% strand | P62992 |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 153 | 35% helix, 18% strand | P68036 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.78 | 0.80 | 86 | empty |
| 2 | 55 | 0.65 | 0.94 | 15 | empty |
| 3 | 157 | 0.60 | 0.84 | 28 | empty |
| 4 | 55 | 0.53 | 0.88 | 19 | empty |
| 5 | 160 | 0.49 | 0.78 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1587 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6DJX · Crystal Structure of pParkin-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 0.96
- 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 6DJX · PDBe 6DJX · UniProt A0A034W4L8 · UniProt P62992 · UniProt P68036
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