9JGP | pdb_00009jgp

Structure of Pd ions bound to human heavy chain ferritin nanocage.

PDB DOI: https://doi.org/10.2210/pdb9JGP/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia phage EcSzw-2
Mutation(s): Yes

Deposited: 2024-09-08 Released: 2025-09-10
Deposition Author(s): Liu, Y.J., Zhao, M., Hu, X.Y., Kang, H.L., Liu, Q.Q., Huang, X.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.184 (Depositor), 0.189 (DCC)
R-Value Work:
0.173 (Depositor), 0.178 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of Pd ions bound to human heavy chain ferritin nanocage.

Hu, X.Y., Kang, H.L., Liu, Q.Q., Zhao, M., Li, Y.K., Peng, W.C., Qi, T.Y., Liu, R.M., Jiao, L., Dou, H.J., Zhuang, J., Liu, Y.J., Mann, S., Huang, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 21.42 kDa
Atom Count: 1,607
Modeled Residue Count: 172
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain, N-terminally processed	A	182	Homo sapiens	Mutation(s): 5 Gene Names: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens) Explore P02794 Go to UniProtKB: P02794
PHAROS: P02794 GTEx: ENSG00000167996
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD Query on PD Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.184 (Depositor), 0.189 (DCC)
R-Value Work: 0.173 (Depositor), 0.178 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.7	α = 90
b = 183.7	β = 90
c = 183.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271448
National Natural Science Foundation of China (NSFC)	China	82072054
National Natural Science Foundation of China (NSFC)	China	21877065
National Natural Science Foundation of China (NSFC)	China	82111530210