Research workbench
Crystal structure of human KDM4C catalytic domain bound to tris
Analyse Crystal structure of human KDM4C catalytic domain bound to tris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDP
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.07
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4C
- EC
- 1.14.11.-
- UniProt
- Q9H3R0
- Ligands
- ZN, FE, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.07 · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4C (EC 1.14.11.-) | protein | 338 | 30% helix, 25% strand | Q9H3R0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.75 | 0.84 | 46 | FE, TRS |
| 2 | 469 | 0.74 | 0.83 | 46 | FE, TRS |
| 3 | 349 | 0.56 | 0.75 | 42 | empty |
| 4 | 94 | 0.51 | 0.83 | 28 | empty |
| 5 | 78 | 0.50 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 420 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4XDP · Crystal structure of human KDM4C catalytic domain bound to tris · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3R0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4C (Q9H3R0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9H3R0
- Elsewhere: RCSB PDB 4XDP · PDBe 4XDP · UniProt Q9H3R0
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