Research workbench
Crystal structure of UBE2K and K48-linked di-ubiquitin complex
Analyse Crystal structure of UBE2K and K48-linked di-ubiquitin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IF1
- Type
- protein
- Length
- 550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 K; Ubiquitin
- EC
- 2.3.2.23
- UniProt
- P61086, P0CG47
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) | protein | 199 | 45% helix, 13% strand | P61086 |
| C, D | Ubiquitin | protein | 76 | 20% helix, 29% strand | P0CG47 |
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 | 852 | 0.69 | 0.75 | 77 | empty |
| 2 | 122 | 0.49 | 0.79 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–D · 447 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 210 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 72 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6IF1 · Crystal structure of Ube2K and K48-linked di-ubiquitin complex · the same entry in another collection · chain A against A, TM-score 1.00
- P61086 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 K (P61086) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P61086
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6IF1 · PDBe 6IF1 · UniProt P61086 · UniProt P0CG47
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