MolNFT v1 · #119454 · protein
Crystal structure of human JARID1C in complex with KDM5-C49
5FWJ · Histone demethylase JARID1C: “Crystal structure of human JARID1C in complex with KDM5-C49”. X-ray diffraction, 4 ligands (MMK, MG, ZN), 11 pockets (best druggability 0.75). MolNFT v1 #119454 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FWJ
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase JARID1C
- EC
- 1.14.11.-
- UniProt
- P41229
- Ligands
- MMK, MG, ZN, MN
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase JARID1C (EC 1.14.11.-) | protein | 435 | 39% helix, 20% strand | P41229 |
| B | Histone demethylase JARID1C (EC 1.14.11.-) | protein | 429 | 40% helix, 21% strand | P41229 |
Ligands and binding sites
- MMK · 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.75 | 0.78 | 103 | empty |
| 2 | 146 | 0.70 | 0.89 | 24 | empty |
| 3 | 145 | 0.68 | 0.88 | 24 | empty |
| 4 | 210 | 0.59 | 0.80 | 30 | MN, MMK |
| 5 | 165 | 0.57 | 0.82 | 27 | MN, MMK |
Interfaces
1 interface between chains.
- A–B · 596 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5FWJ · Crystal structure of human JARID1C in complex with KDM5-C49 · the same entry in another collection · chain A against A, TM-score 1.00
- P41229 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5C (P41229) · 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 P41229
- Elsewhere: RCSB PDB 5FWJ · PDBe 5FWJ · UniProt P41229
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