Research workbench
Crystal structure of raphanus sativus AGDP1 AGD12 in complex with an H3K9ME2 peptide
Analyse Crystal structure of raphanus sativus AGDP1 AGD12 in complex with an H3K9ME2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZWX
- Type
- protein
- Length
- 316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF724 domain-containing protein 6-like; H3(1-15)K9ME2 peptide
- UniProt
- P59226
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DUF724 domain-containing protein 6-like | protein | 148 | 9% helix, 46% strand | — |
| P, Q | H3(1-15)K9ME2 peptide | protein | 10 | 40% helix, 0% strand | P59226 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.65 | 0.81 | 33 | empty |
| 2 | 52 | 0.38 | 0.81 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–Q · 683 Ų buried · 12 hydrogen bonds · protein-protein
- A–P · 680 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 411 Ų buried · 10 hydrogen bonds · protein-protein
- A–Q · 234 Ų buried · 2 hydrogen bonds · protein-protein
- P–B · 200 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered, methylation).
Compared structures
- 5ZWX · Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.49
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 P59226
- Elsewhere: RCSB PDB 5ZWX · PDBe 5ZWX · UniProt P59226
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.