Research workbench
Crystal structure of ring E3 ligase ZNRF1 in complex with UBE2N (UBC13)
Analyse Crystal structure of ring E3 ligase ZNRF1 in complex with UBE2N (UBC13) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YWR
- Type
- protein
- Length
- 237 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 N; E3 ubiquitin-protein ligase ZNRF1
- EC
- 2.3.2.23, 2.3.2.27
- UniProt
- P61088, Q8ND25
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 150 | 34% helix, 17% strand | P61088 |
| B | E3 ubiquitin-protein ligase ZNRF1 (EC 2.3.2.27) | protein | 87 | 22% helix, 20% strand | Q8ND25 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains B
- PGE · Triethylene glycol · additive · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.45 | 0.74 | 29 | empty |
| 2 | 75 | 0.33 | 0.75 | 23 | FMT |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5YWR · Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13) · the same entry in another collection · chain A against A, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8ND25 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ZNRF1 (Q8ND25) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P61088
- Every structure of UniProt Q8ND25
- Elsewhere: RCSB PDB 5YWR · PDBe 5YWR · UniProt P61088 · UniProt Q8ND25
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