MolNFT v1 · #163647 · protein
Crystal structure of the catalytic domain of UBE2S wt.
6S98 · Ubiquitin-conjugating enzyme E2 S: “Crystal structure of the catalytic domain of UBE2S wt.”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.60). MolNFT v1 #163647 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6S98
- Type
- protein
- Length
- 299 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
- NA
- Pockets
- 2 · best druggability 0.60
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 | 148 | 41% helix, 17% strand | Q16763 |
| B | Ubiquitin-conjugating enzyme E2 S (EC 2.3.2.23) | protein | 151 | 40% helix, 17% strand | Q16763 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.60 | 0.78 | 39 | ACT, EDO |
| 2 | 60 | 0.34 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1174 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (oxidation, disulfide).
Compared structures
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 6S98 · PDBe 6S98 · UniProt Q16763
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