MolNFT v1 · #141471 · protein
Crystal structure of arabidopsis thaliana ebs in complex with an H3K27ME3 peptide
5Z8L · Chromatin remodeling protein ebs: “Crystal structure of arabidopsis thaliana ebs in complex with an H3K27ME3 peptide”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.49). MolNFT v1 #141471 on GenesisL1: 3D…
- 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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