Research workbench
CEKDM7A from C.ELEGANS, complex with H3K4ME3 peptide, H3K9ME2 peptide and nog
Analyse CEKDM7A from C.ELEGANS, complex with H3K4ME3 peptide, H3K9ME2 peptide and nog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N9O
- Type
- protein
- Length
- 497 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; Histone H3 peptide
- EC
- 1.14.11.27
- UniProt
- Q9GYI0, P08898
- Ligands
- OGA, ZN, FE2
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein (EC 1.14.11.27) | protein | 483 | 41% helix, 20% strand | Q9GYI0 |
| B | Histone H3 peptide | protein | 6 | 0% helix, 50% strand | P08898 |
| C | Histone H3 peptide | protein | 8 | 0% helix, 0% strand | P08898 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A
- FE2 · Fe (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.71 | 0.98 | 15 | FE2, OGA |
| 2 | 92 | 0.58 | 0.87 | 19 | empty |
| 3 | 193 | 0.54 | 0.79 | 26 | empty |
| 4 | 175 | 0.48 | 0.76 | 22 | empty |
| 5 | 204 | 0.47 | 0.74 | 36 | empty |
Interfaces
2 interfaces between chains.
- A–C · 865 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3N9O · ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K9me2 peptide and NOG · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GYI0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 7 homolog (Q9GYI0) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P08898 · AlphaFold monomer V2.0 prediction for histone H3 (P08898) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 Q9GYI0
- Every structure of UniProt P08898
- Elsewhere: RCSB PDB 3N9O · PDBe 3N9O · UniProt Q9GYI0 · UniProt P08898
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