Research workbench
PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09552a
Analyse PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PH8
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.396
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4D
- UniProt
- Q6B0I6
- Ligands
- OGA, PHT, 1XN, ZN, NI, SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.396 · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D | protein | 331 | 32% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- PHT · Phthalic acid · ligand · chains A
- 1XN · 2H-isoindole-1,3-diamine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 394 | 0.75 | 0.85 | 48 | NI, OGA, EDO |
| 2 | 76 | 0.35 | 0.76 | 25 | EDO |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5PH8 · Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09552A · the same entry in another collection · chain A against A, TM-score 1.00
- Q6B0I6 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4D (Q6B0I6) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 5PH8 · PDBe 5PH8 · UniProt Q6B0I6
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