Research workbench
Crystal structure of the jumonji domain of human jumonji domain containing 1C protein
Analyse Crystal structure of the jumonji domain of human jumonji domain containing 1C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPD
- Type
- protein
- Length
- 653 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable jmjc domain-containing histone demethylation prot ein 2C
- EC
- 1.14.11.-
- UniProt
- Q15652
- Ligands
- EMT, NA
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable jmjc domain-containing histone demethylation prot ein 2C (EC 1.14.11.-) | protein | 327 | 36% helix, 22% strand | Q15652 |
| B | Probable jmjc domain-containing histone demethylation prot ein 2C (EC 1.14.11.-) | protein | 326 | 36% helix, 22% strand | Q15652 |
Ligands and binding sites
- EMT · 2-(ethylmercuri-thio)-benzoic acid · ligand · 11 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.64 | 0.82 | 37 | EMT |
| 2 | 176 | 0.62 | 0.84 | 24 | EMT |
| 3 | 418 | 0.59 | 0.75 | 51 | empty |
| 4 | 84 | 0.48 | 0.82 | 19 | empty |
| 5 | 50 | 0.46 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 297 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YPD · Crystal structure of the Jumonji domain of human Jumonji domain containing 1C protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q15652 · AlphaFold monomer V2.0 prediction for probable jmjc domain-containing histone… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q15652
- Elsewhere: RCSB PDB 2YPD · PDBe 2YPD · UniProt Q15652
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