MolNFT v1 · #116500 · protein
Crystal structure of UBE2K~UBIQUITIN conjugate
5DFL: “Crystal structure of UBE2K~UBIQUITIN conjugate”. X-ray diffraction, 1 pocket (best druggability 0.25). MolNFT v1 #116500 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DFL
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Ubiquitin-conjugating enzyme E2 K
- EC
- 6.3.2.19
- UniProt
- P0CG47, P61086
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin | protein | 76 | 24% helix, 33% strand | P0CG47 |
| A | Ubiquitin-conjugating enzyme E2 K (EC 6.3.2.19) | protein | 199 | 46% helix, 14% strand | P61086 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.25 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 113 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
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 P0CG47
- Every structure of UniProt P61086
- Elsewhere: RCSB PDB 5DFL · PDBe 5DFL · UniProt P0CG47 · UniProt P61086
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