Research workbench
E2 UBE2K covalently linked to donor ub, acceptor di-ub, and ring E3 primed for K48-linked ub chain synthesis
Analyse E2 UBE2K covalently linked to donor ub, acceptor di-ub, and ring E3 primed for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OJX
- Type
- protein
- Length
- 488 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF38; Ubiquitin-conjugating enzyme E2 K; Polyubiquitin-B
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- Q9H0F5, P61086, P0CG47
- Ligands
- ME7, ZN
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF38 (EC 2.3.2.27) | protein | 68 | 15% helix, 24% strand | Q9H0F5 |
| B | Ubiquitin-conjugating enzyme E2 K (EC 2.3.2.23) | protein | 196 | 42% helix, 14% strand | P61086 |
| C | Polyubiquitin-B | protein | 76 | 20% helix, 34% strand | P0CG47 |
| D | Polyubiquitin-B | protein | 76 | 24% helix, 34% strand | P0CG47 |
| E | Polyubiquitin-B | protein | 72 | 17% helix, 35% strand | P0CG47 |
Ligands and binding sites
- ME7 · 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) · ligand · chains B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.60 | 0.79 | 37 | empty |
| 2 | 270 | 0.59 | 0.79 | 35 | empty |
| 3 | 120 | 0.47 | 0.79 | 23 | empty |
| 4 | 131 | 0.46 | 0.78 | 27 | empty |
| 5 | 144 | 0.39 | 0.73 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–C · 828 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 637 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 201 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 7OJX · E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked… · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.97
- Q9H0F5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF38 (Q9H0F5) · 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 Q9H0F5
- Every structure of UniProt P61086
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 7OJX · PDBe 7OJX · UniProt Q9H0F5 · UniProt P61086 · UniProt P0CG47
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