Research workbench
Pao-linked dimer of the catalytic domain of the human ubiquitin- conjugating enzyme UBE2S
Analyse Pao-linked dimer of the catalytic domain of the human ubiquitin- conjugating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QHK
- Type
- protein
- Length
- 297 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
- Ligands
- PA0, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) | protein | 147 | 41% helix, 17% strand | Q16763 |
| B | Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) | protein | 150 | 41% helix, 17% strand | Q16763 |
Ligands and binding sites
- PA0 · Phenylarsine oxide · ligand · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 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 | 223 | 0.69 | 0.86 | 28 | PA0 |
| 2 | 113 | 0.53 | 0.82 | 24 | empty |
| 3 | 124 | 0.47 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6QHK · PAO-linked dimer of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.96
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 6QHK · PDBe 6QHK · UniProt Q16763
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.