MolNFT v1 · #141472 · protein
Crystal structure of arabidopsis thaliana ebs C-terminal deletion construct in complex with an H3K4ME2 peptide
5Z8N · Chromatin remodeling protein ebs: “Crystal structure of arabidopsis thaliana ebs C-terminal deletion construct in complex with an H3K4ME2 peptide”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.41). MolNFT v1…
- PDB
- 5Z8N
- Type
- protein
- Length
- 567 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromatin remodeling protein ebs; H3K4ME2 peptide
- UniProt
- F4JL28, P59226
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chromatin remodeling protein ebs | protein | 183 | 10% helix, 40% strand | F4JL28 |
| P | H3K4ME2 peptide | protein | 5 | 0% helix, 20% strand | P59226 |
| B | Chromatin remodeling protein ebs | protein | 182 | 8% helix, 37% strand | F4JL28 |
| Q, R | H3K4ME2 peptide | protein | 7 | 0% helix, 29% strand | P59226 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.41 | 0.75 | 21 | empty |
| 2 | 55 | 0.38 | 0.80 | 15 | empty |
| 3 | 118 | 0.38 | 0.74 | 17 | empty |
| 4 | 66 | 0.37 | 0.78 | 11 | empty |
| 5 | 71 | 0.34 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–Q · 620 Ų buried · 9 hydrogen bonds · protein-protein
- C–R · 611 Ų buried · 12 hydrogen bonds · protein-protein
- A–P · 509 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 5Z8N · Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex… · the same entry in another collection · chain R against R, TM-score 1.00
- F4JL28 · AlphaFold monomer V2.0 prediction for chromatin remodeling protein ebs (F4JL28) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.87
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 5Z8N · PDBe 5Z8N · UniProt F4JL28 · UniProt P59226
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