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Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin- protein ligase mex-3C
Analyse Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin- protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WWZ
- Type
- protein
- Length
- 237 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-binding E3 ubiquitin-protein ligase MEX3C
- EC
- 2.3.2.27
- UniProt
- Q5U5Q3
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | RNA-binding E3 ubiquitin-protein ligase MEX3C (EC 2.3.2.27) | protein | 80 | 43% helix, 19% strand | Q5U5Q3 |
| A | RNA-binding E3 ubiquitin-protein ligase MEX3C (EC 2.3.2.27) | protein | 78 | 45% helix, 26% strand | Q5U5Q3 |
| C | RNA-binding E3 ubiquitin-protein ligase MEX3C (EC 2.3.2.27) | protein | 79 | 43% helix, 25% strand | Q5U5Q3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.62 | 0.79 | 34 | SO4 |
| 2 | 73 | 0.30 | 0.73 | 18 | empty |
| 3 | 59 | 0.30 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 872 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 558 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WWZ · Crystal structure of the KH2 domain of human RNA-binding E3 ubiquitin-protein ligase… · the same entry in another collection · chain B against B, TM-score 1.00
- Q5U5Q3 · AlphaFold monomer V2.0 prediction for RNA-binding E3 ubiquitin- protein ligase MEX3C… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q5U5Q3
- Elsewhere: RCSB PDB 5WWZ · PDBe 5WWZ · UniProt Q5U5Q3
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