MolNFT v1 · #87726 · protein
Xenopus ZNRF3 ectodomain in complex with xenopus RSPO2 FU1- FU2 crystal form I
4C9R · E3 ubiquitin-protein ligase ZNRF3: “Xenopus ZNRF3 ectodomain in complex with xenopus RSPO2 FU1- FU2 crystal form I”. X-ray diffraction, 8 pockets (best druggability 0.72). MolNFT v1 #87726 on GenesisL1: 3D structure, binding sites…
- PDB
- 4C9R
- Type
- protein
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase ZNRF3; R-spondin-2
- EC
- 6.3.2.-
- UniProt
- Q08D68, Q5M7L6
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-) | protein | 161 | 22% helix, 32% strand | Q08D68 |
| B | R-spondin-2 | protein | 105 | 0% helix, 53% strand | Q5M7L6 |
| D | R-spondin-2 | protein | 107 | 0% helix, 51% strand | Q5M7L6 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.72 | 0.89 | 36 | empty |
| 2 | 320 | 0.71 | 0.84 | 44 | empty |
| 3 | 129 | 0.55 | 0.82 | 19 | empty |
| 4 | 119 | 0.55 | 0.83 | 19 | empty |
| 5 | 131 | 0.48 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1272 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1159 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4C9R · Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form I · the same entry in another collection · chain A against A, TM-score 1.00
- Q08D68 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ZNRF3 (Q08D68) · a predicted model of the same protein · chain A against A, TM-score 0.91
- Q5M7L6 · AlphaFold monomer V2.0 prediction for R-spondin-2 (Q5M7L6) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 Q08D68
- Every structure of UniProt Q5M7L6
- Elsewhere: RCSB PDB 4C9R · PDBe 4C9R · UniProt Q08D68 · UniProt Q5M7L6
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