MolNFT v1 · #79264 · protein
Crystal structure of the salmonella E3 ubiquitin ligase sopa in complex with the human E2 UBCH7
3SY2 · E3 ubiquitin-protein ligase sopa: “Crystal structure of the salmonella E3 ubiquitin ligase sopa in complex with the human E2 UBCH7”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v1 #79264 on…
- PDB
- 3SY2
- Type
- protein
- Length
- 1,533 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase sopa; Ubiquitin-conjugating enzyme E2 L3
- EC
- 6.3.2.-, 6.3.2.19
- UniProt
- Q8ZNR3, P68036
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase sopa (EC 6.3.2.-) | protein | 609 | 43% helix, 7% strand | Q8ZNR3 |
| B | E3 ubiquitin-protein ligase sopa (EC 6.3.2.-) | protein | 616 | 47% helix, 10% strand | Q8ZNR3 |
| C, D | Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) | protein | 154 | 34% helix, 15% strand | P68036 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.82 | 0.92 | 43 | empty |
| 2 | 699 | 0.81 | 0.85 | 55 | empty |
| 3 | 526 | 0.80 | 0.87 | 38 | empty |
| 4 | 255 | 0.60 | 0.80 | 39 | empty |
| 5 | 62 | 0.57 | 0.89 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–D · 688 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 658 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 274 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SY2 · Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2… · 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 0.98
- Q8ZNR3 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase sopa (Q8ZNR3) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q8ZNR3
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 3SY2 · PDBe 3SY2 · UniProt Q8ZNR3 · UniProt P68036
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