Research workbench
Crystal structure of arabidopsis thaliana ebs in complex with an H3K27ME3 peptide
Analyse Crystal structure of arabidopsis thaliana ebs in complex with an H3K27ME3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z8L
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromatin remodeling protein ebs; H3K27ME3 peptide
- UniProt
- F4JL28, P59226
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chromatin remodeling protein ebs | protein | 204 | 12% helix, 34% strand | F4JL28 |
| P | H3K27ME3 peptide | protein | 8 | 0% helix, 0% strand | P59226 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.49 | 0.77 | 23 | empty |
| 2 | 78 | 0.37 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–P · 563 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 5Z8L · crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- F4JL28 · AlphaFold monomer V2.0 prediction for chromatin remodeling protein ebs (F4JL28) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.51
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 F4JL28
- Every structure of UniProt P59226
- Elsewhere: RCSB PDB 5Z8L · PDBe 5Z8L · UniProt F4JL28 · UniProt P59226
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