Research workbench
Xenopus ZNRF3 ectodomain in complex with xenopus RSPO2 FU1-FU2 crystal form II
Analyse Xenopus ZNRF3 ectodomain in complex with xenopus RSPO2 FU1-FU2 crystal form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C9U
- Type
- protein
- Length
- 505 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 0.74
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-) | protein | 161 | 18% helix, 34% strand | Q08D68 |
| B | R-spondin-2 | protein | 103 | 0% helix, 50% strand | Q5M7L6 |
| C | E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-) | protein | 155 | 19% helix, 35% strand | Q08D68 |
| D | R-spondin-2 | protein | 86 | 0% helix, 51% strand | Q5M7L6 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.74 | 0.84 | 50 | empty |
| 2 | 191 | 0.68 | 0.87 | 33 | empty |
| 3 | 269 | 0.66 | 0.82 | 37 | empty |
| 4 | 151 | 0.62 | 0.84 | 23 | empty |
| 5 | 104 | 0.53 | 0.83 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1104 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1088 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 230 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 165 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 4C9U · Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II · the same entry in another collection · chain D against D, 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 C 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 D against A, TM-score 0.86
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 4C9U · PDBe 4C9U · UniProt Q08D68 · UniProt Q5M7L6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.