MolNFT v1 · #119556 · protein
Crystal structure of the catalytic domain of human JMJD1C
5FZO · Probable jmjc domain-containing histone demethylation prot…: “Crystal structure of the catalytic domain of human JMJD1C”. X-ray diffraction, 2 ligands (MN, CL), 8 pockets (best druggability 0.68). MolNFT v1 #119556 on GenesisL1: 3D…
- PDB
- 5FZO
- Type
- protein
- Length
- 678 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
- MN, CL
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% 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 | 339 | 35% helix, 22% strand | Q15652 |
| B | Probable jmjc domain-containing histone demethylation prot ein 2C (EC 1.14.11.-) | protein | 339 | 35% helix, 22% strand | Q15652 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.68 | 0.83 | 45 | MN |
| 2 | 324 | 0.66 | 0.81 | 39 | MN, EDO |
| 3 | 394 | 0.60 | 0.76 | 52 | empty |
| 4 | 181 | 0.60 | 0.82 | 27 | empty |
| 5 | 118 | 0.44 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 307 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5FZO · Crystal structure of the catalytic domain of human JmjD1C · 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 5FZO · PDBe 5FZO · UniProt Q15652
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