MolNFT v1 · #55595 · protein
Crystal structure of the jumonji domain of human jumonji domain containing 1C protein
2YPD · Probable jmjc domain-containing histone demethylation prot…: “Crystal structure of the jumonji domain of human jumonji domain containing 1C protein”. X-ray diffraction, 2 ligands (EMT, NA), 12 pockets (best druggability 0.64).…
- 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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