MolNFT v1 · #109808 · protein
Crystal structure of human KDM4C catalytic domain with oga
4XDO · Lysine-specific demethylase 4C: “Crystal structure of human KDM4C catalytic domain with oga”. X-ray diffraction, 3 ligands (OGA, ZN, FE), 6 pockets (best druggability 0.73). MolNFT v1 #109808 on GenesisL1: 3D structure, binding…
- PDB
- 4XDO
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4C
- EC
- 1.14.11.-
- UniProt
- Q9H3R0
- Ligands
- OGA, ZN, FE
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4C (EC 1.14.11.-) | protein | 338 | 31% helix, 25% strand | Q9H3R0 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 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 | 408 | 0.73 | 0.83 | 40 | OGA |
| 2 | 431 | 0.71 | 0.82 | 43 | OGA |
| 3 | 398 | 0.62 | 0.77 | 51 | empty |
| 4 | 73 | 0.51 | 0.84 | 24 | empty |
| 5 | 89 | 0.50 | 0.83 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4XDO · Crystal structure of human KDM4C catalytic domain with OGA · 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 4XDO · PDBe 4XDO · UniProt Q9H3R0
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