MolNFT v1 · #95114 · protein
Histone H3 lysine 4 demethylating rice JMJ703 in complex with methylated H3K4 substrate
4IGQ · OS05G0196500 protein: “Histone H3 lysine 4 demethylating rice JMJ703 in complex with methylated H3K4 substrate”. X-ray diffraction, 2 ligands (OGA, FE), 3 pockets (best druggability 0.72). MolNFT v1 #95114 on GenesisL1: 3D…
- PDB
- 4IGQ
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OS05G0196500 protein; Mathylated H3K4 substrate
- UniProt
- Q53WJ1
- Ligands
- OGA, FE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OS05G0196500 protein | protein | 273 | 35% helix, 28% strand | Q53WJ1 |
| B | Mathylated H3K4 substrate | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.72 | 0.91 | 31 | FE, OGA |
| 2 | 130 | 0.45 | 0.77 | 16 | empty |
| 3 | 65 | 0.37 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4IGQ · Histone H3 Lysine 4 Demethylating Rice JMJ703 in complex with methylated H3K4 substrate · the same entry in another collection · chain A against A, TM-score 1.00
- Q53WJ1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase JMJ703 (Q53WJ1) · 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 Q53WJ1
- Elsewhere: RCSB PDB 4IGQ · PDBe 4IGQ · UniProt Q53WJ1
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