Research workbench
Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7
Analyse Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQV
- Type
- protein
- Length
- 1,511 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Escherichia coli; Homo sapiens
- Molecule
- secreted effector protein; Ubiquitin-conjugating enzyme E2 L3
- EC
- 6.3.2.19
- UniProt
- Q8X5G6, P68036
- Ligands
- SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.3 · 3 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | secreted effector protein (EC 6.3.2.19) | protein | 606 | 40% helix, 8% strand | Q8X5G6 |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) | protein | 147 | 29% helix, 11% strand | P68036 |
| D | Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) | protein | 152 | 28% helix, 12% strand | P68036 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.84 | 0.85 | 82 | empty |
| 2 | 1113 | 0.83 | 0.84 | 135 | empty |
| 3 | 1107 | 0.82 | 0.83 | 115 | empty |
| 4 | 341 | 0.75 | 0.86 | 49 | empty |
| 5 | 422 | 0.74 | 0.83 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1945 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1014 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 843 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3SQV · Crystal structure of E. COLI O157:H7 E3 ubiquitin ligase, nlel, with a human E2, UBCH7 · 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 D against A, TM-score 0.95
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 Q8X5G6
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 3SQV · PDBe 3SQV · UniProt Q8X5G6 · UniProt P68036
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