MolNFT v2 · #131120 · protein
PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 106)
5PKL: “PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand…”. X-ray diffraction at 1.35, 5 ligands (OGA, ZN, NI). MolNFT v2 #131120 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5PKL
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.35
- Source
- Homo sapiens
- UniProt
- Q6B0I6
- Ligands
- OGA, ZN, NI, MG, SO4
Structure
x-ray diffraction · resolution 1.35 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 331 | — | 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.
Compared structures
- 5PKL · 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 5PKL · PDBe 5PKL · UniProt Q6B0I6
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