Research workbench
Crystal structure of PHF2 phd domain complexed with H3K4ME3 peptide
Analyse Crystal structure of PHF2 phd domain complexed with H3K4ME3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KQI
- Type
- protein
- Length
- 77 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 2; H3K4ME3 peptide
- UniProt
- O75151, P68431
- Ligands
- ZN, MG, CL
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 2 | protein | 71 | 20% helix, 17% strand | O75151 |
| B | H3K4ME3 peptide | protein | 6 | 0% helix, 33% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 524 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3KQI · crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- O75151 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase PHF2 (O75151) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 O75151
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 3KQI · PDBe 3KQI · UniProt O75151 · UniProt P68431
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