MolNFT v1 · #65036 · protein
Crystal structure of JARID1A-PHD3 complexed with H3(1-9) K4ME3 peptide
3GL6 · Histone demethylase JARID1A: “Crystal structure of JARID1A-PHD3 complexed with H3(1-9) K4ME3 peptide”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #65036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GL6
- Type
- protein
- Length
- 60 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone demethylase JARID1A; Histone H3
- EC
- 1.14.11.-
- UniProt
- P29375
- Ligands
- ZN
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone demethylase JARID1A (EC 1.14.11.-) | protein | 52 | 17% helix, 17% strand | P29375 |
| B | Histone H3 | protein | 8 | 0% helix, 63% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3GL6 · Crystal structure of JARID1A-PHD3 complexed with H3(1-9)K4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 P29375
- Elsewhere: RCSB PDB 3GL6 · PDBe 3GL6 · UniProt P29375
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