MolNFT v1 · #94175 · protein
Crystal structure of human JMJD2D/KDM4D in complex with an H3K9ME3 peptide and 2-oxoglutarate
4HON · Lysine-specific demethylase 4D: “Crystal structure of human JMJD2D/KDM4D in complex with an H3K9ME3 peptide and 2-oxoglutarate”. X-ray diffraction, 5 ligands (AKG, NI, ZN), 6 pockets (best druggability 0.78). MolNFT v1 #94175 on…
- PDB
- 4HON
- Type
- protein
- Length
- 677 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D; Histone H3 peptide
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- AKG, NI, ZN, NO3, SCN
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 330 | 30% helix, 26% strand | Q6B0I6 |
| F | Histone H3 peptide | protein | 10 | 0% helix, 10% strand | — |
| G | Histone H3 peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, F, B, G
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, G
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 12 copies · chains A, F, B
- SCN · Thiocyanate ion · ion · 6 copies · chains A, B
- PDO · 1,3-propandiol · additive · 5 copies · chains A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.78 | 0.79 | 80 | PDO |
| 2 | 69 | 0.75 | 0.99 | 20 | AKG, NI |
| 3 | 59 | 0.72 | 0.98 | 19 | AKG, PDO |
| 4 | 160 | 0.49 | 0.78 | 29 | NO3 |
| 5 | 51 | 0.44 | 0.84 | 16 | NO3 |
Interfaces
3 interfaces between chains.
- A–F · 726 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 591 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 389 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4HON · Crystal structure of human JMJD2D/KDM4D in complex with an H3K9me3 peptide and… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6B0I6
- Elsewhere: RCSB PDB 4HON · PDBe 4HON · UniProt Q6B0I6
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