Research workbench
Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M
Analyse Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QH3
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 S
- EC
- 2.3.2.23
- UniProt
- Q16763
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) | protein | 147 | 41% helix, 20% strand | Q16763 |
| A | Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) | protein | 148 | 43% helix, 18% strand | Q16763 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.72 | 0.87 | 31 | EDO |
| 2 | 358 | 0.62 | 0.78 | 39 | EDO |
| 3 | 50 | 0.46 | 0.85 | 13 | EDO |
| 4 | 88 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 793 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6QH3 · Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M · the same entry in another collection · chain B against B, TM-score 1.00
- Q16763 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 S (Q16763) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q16763
- Elsewhere: RCSB PDB 6QH3 · PDBe 6QH3 · UniProt Q16763
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