MolNFT v1 · #142211 · protein
Crystal structure of raphanus sativus AGDP1 AGD12 in complex with an H3K9ME2 peptide
5ZWX · DUF724 domain-containing protein 6-like: “Crystal structure of raphanus sativus AGDP1 AGD12 in complex with an H3K9ME2 peptide”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #142211 on GenesisL1: 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
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