MolNFT v1 · #59731 · protein
Crystal structure of the ING5 phd finger in complex with H3K4ME3 peptide
3C6W · Inhibitor of growth protein 5: “Crystal structure of the ING5 phd finger in complex with H3K4ME3 peptide”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #59731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.