Research workbench
Crystal structure of the ING5 phd finger in complex with H3K4ME3 peptide
Analyse Crystal structure of the ING5 phd finger in complex 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
- 3C6W
- Type
- protein
- Length
- 121 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inhibitor of growth protein 5; H3K4ME3 histone peptide
- UniProt
- Q8WYH8
- Ligands
- ZN
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inhibitor of growth protein 5 | protein | 51 | 14% helix, 22% strand | Q8WYH8 |
| B | H3K4ME3 histone peptide | protein | 7 | 0% helix, 43% strand | — |
| C | Inhibitor of growth protein 5 | protein | 52 | 13% helix, 15% strand | Q8WYH8 |
| D | H3K4ME3 histone peptide | protein | 11 | 0% helix, 27% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- C–D · 687 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 155 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3C6W · Crystal structure of the ING5 PHD finger in complex with H3K4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WYH8 · AlphaFold monomer V2.0 prediction for inhibitor of growth protein 5 (Q8WYH8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8WYH8
- Elsewhere: RCSB PDB 3C6W · PDBe 3C6W · UniProt Q8WYH8
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