Research workbench
Crystal structure of the salmonella E3 ubiquitin ligase sopa in complex with the human E2 UBCH7
Analyse Crystal structure of the salmonella E3 ubiquitin ligase sopa in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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