Research workbench
Structual basis for the recognition of UBC13 by the shigella flexneri effector ospi
Analyse Structual basis for the recognition of UBC13 by the shigella flexneri effector… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W31
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF169B; Ubiquitin-conjugating enzyme E2 N
- EC
- 6.3.2.19
- UniProt
- Q8VSD5, P61088
- Ligands
- IOD
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ORF169B | protein | 192 | 39% helix, 15% strand | Q8VSD5 |
| B | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 152 | 34% helix, 18% strand | P61088 |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.60 | 0.86 | 19 | empty |
| 2 | 121 | 0.53 | 0.82 | 27 | empty |
| 3 | 81 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1004 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3W31 · Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI · the same entry in another collection · chain A against A, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q8VSD5
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 3W31 · PDBe 3W31 · UniProt Q8VSD5 · UniProt P61088
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