MolNFT v1 · #141119 · protein
Crystal structure of ring E3 ligase ZNRF1 in complex with UBE2N (UBC13)
5YWR · Ubiquitin-conjugating enzyme E2 N: “Crystal structure of ring E3 ligase ZNRF1 in complex with UBE2N (UBC13)”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.45). MolNFT v1 #141119 on GenesisL1: 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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