MolNFT v1 · #130690 · protein
Pandda analysis group deposition -- crystal structure of JMJD2D after initial refinement with no ligand modelled (structure 89)
5PK4 · Lysine-specific demethylase 4D: “Pandda analysis group deposition -- crystal structure of JMJD2D after initial refinement with no ligand…”. X-ray diffraction, 5 ligands (OGA, ZN, NI), 3 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 5PK4
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D
- UniProt
- Q6B0I6
- Ligands
- OGA, ZN, NI, MG, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D | protein | 331 | 31% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NI · Nickel (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.75 | 0.84 | 51 | NI, OGA, EDO |
| 2 | 53 | 0.47 | 0.85 | 17 | EDO |
| 3 | 73 | 0.36 | 0.77 | 26 | EDO |
Compared structures
- 5PK4 · PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement… · 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 5PK4 · PDBe 5PK4 · UniProt Q6B0I6
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