9JGP: Pd ions

Structure of Pd ions bound to human heavy chain ferritin nanocage. Determined by X-ray diffraction at 1.53 Å resolution. Released 10 Sept 2025.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,607
Mol. weight: 21.42 kDa
Ligands: PD, MG
Released: 10 Sept 2025

Explore 9JGP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JGP contains 8 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	14-41	28
α-helix	49-76	28
α-helix	86-88	3
α-helix	96-123	28
α-helix	127-133	7
α-helix	134-138	5
α-helix	139-158	20
α-helix	164-173	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ferritin heavy chain, N-terminally processed	A	protein	182	Homo sapiens	P02794 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JGP_1 Ferritin heavy chain, N-terminally processed (chains A)
TTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSASYYFDRDDVALKNFAKYFLHQSH
EEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWESGLNAMEAALQLEKNVNQSLLELHAL
ATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGDSDN
ES

Ligands and cofactors

ID	Name	Formula	Copies
PD	Palladium ion	Pd	2
MG	Magnesium ion	Mg	4

Water and common crystallization additives (NA) are not listed.

Primary citation

Granzyme B-mimetic nanozyme for nanovesicle targeted anticancer applications. Hu, X., Liu, Q., Kang, H. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-68773-x · PubMed

Other PDB entries of the same protein (UniProt P02794 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6B8F 1.06 Å, Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid
6B8G 1.13 Å, Twice-Contracted Human Heavy-Chain Ferritin Crystal-Hydrogel Hybrid
7A6A 1.15 Å, 1.15 A structure of human apoferritin obtained from Titan Mono- BCOR microscope
8B7O 1.17 Å, X-ray structure of Auranofin-human H-chain ferritin
6WYF 1.25 Å, Crystal structure of Human H-chain Ferritin variant 157C Delta C-star Modified with a…
6Z6U 1.25 Å, 1.25 A structure of human apoferritin obtained from Titan Mono-BCOR microscope
7RRP 1.27 Å, Apoferritin structure at 1.27 angstrom resolution determined from a 300 kV Titan Krios…
7A6B 1.33 Å, 1.33 A structure of human apoferritin obtained from Titan Mono- BCOR microscope
4Y08 1.34 Å, One minute iron loaded human H ferritin
7K3V 1.34 Å, Apoferritin structure at 1.34 angstrom resolution determined from a 300 kV Titan Krios…
7K3W 1.36 Å, Apoferritin structure at 1.36 angstrom resolution determined from a 300 kV Titan Krios…
9RGH 1.38 Å, X-ray structure of a polyoxidovanadate/human H-ferritin adduct obtained when the protein…

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