Research workbench
Mouse ZNRF3 ectodomain in complex with xenopus RSPO2 FU1- FU2 (seleno met) crystal form II
Analyse Mouse ZNRF3 ectodomain in complex with xenopus RSPO2 FU1- FU2 (seleno met)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C9E
- Type
- protein
- Length
- 1,024 residues
- Chains
- 8
- 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
- Q5SSZ7, Q5M7L6
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-) | protein | 153 | 25% helix, 35% strand | Q5SSZ7 |
| B, D | R-spondin-2 | protein | 104 | 0% helix, 41% strand | Q5M7L6 |
| C, G | E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-) | protein | 152 | 24% helix, 39% strand | Q5SSZ7 |
| F, H | R-spondin-2 | protein | 103 | 0% helix, 35% strand | Q5M7L6 |
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.75 | 0.84 | 55 | empty |
| 2 | 765 | 0.73 | 0.79 | 76 | empty |
| 3 | 474 | 0.71 | 0.81 | 50 | empty |
| 4 | 318 | 0.68 | 0.83 | 40 | empty |
| 5 | 130 | 0.65 | 0.87 | 19 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1325 Ų buried · 30 hydrogen bonds · protein-protein
- E–G · 1247 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 1119 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1053 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1041 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 4 modified (disulfide, engineered).
Compared structures
- 4C9E · Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II · the same entry in another collection · chain H against H, TM-score 1.00
- Q5SSZ7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ZNRF3 (Q5SSZ7) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q5M7L6 · AlphaFold monomer V2.0 prediction for R-spondin-2 (Q5M7L6) · a predicted model of the same protein · chain B 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 Q5SSZ7
- Every structure of UniProt Q5M7L6
- Elsewhere: RCSB PDB 4C9E · PDBe 4C9E · UniProt Q5SSZ7 · UniProt Q5M7L6
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