7BD7 | pdb_00007bd7

X-ray structure of Arsenoplatin-1-encapsulated horse spleen ferritin

PDB DOI: https://doi.org/10.2210/pdb7BD7/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Equus caballus
Mutation(s): No

Deposited: 2020-12-21 Released: 2021-03-17
Deposition Author(s): Ferraro, G., Merlino, A.
Funding Organization(s): Italian Association for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.166 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Arsenoplatin-Ferritin Nanocage: Structure and Cytotoxicity.

Ferraro, G., Pratesi, A., Cirri, D., Imbimbo, P., Maria Monti, D., Messori, L., Merlino, A.

(2021) Int J Mol Sci 22

PubMed: 33668605 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms22041874
Primary Citation Related Structures:
7BD7

PubMed Abstract:
Arsenoplatin-1 (AP-1), the prototype of a novel class of metallodrugs containing a PtAs(OH) ₂ core, was encapsulated within the apoferritin (AFt) nanocage. UV-Vis absorption spectroscopy and inductively coupled plasma-atomic emission spectroscopy measurements confirmed metallodrug encapsulation and allowed us to determine the average amount of AP-1 trapped inside the cage. The X-ray structure of AP-1-encapsulated AFt was solved at 1.50 Å. Diffraction data revealed that an AP-1 fragment coordinates the side chain of a His residue. The biological activity of AP-1-loaded AFt was comparatively tested on a few representative cancer and non-cancer cell lines. Even though the presence of the cage reduces the overall cytotoxicity of AP-1, it improves its selectivity towards cancer cells.

Organizational Affiliation

Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia, 3-13, Sesto Fiorentino, 50019 Florence, Italy.

Macromolecule Content

Total Structure Weight: 22.11 kDa
Atom Count: 1,659
Modeled Residue Count: 172
Deposited Residue Count: 172
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin light chain	A	172	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02791 (Equus caballus) Explore P02791 Go to UniProtKB: P02791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A6R (Subject of Investigation/LOI) Query on A6R Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	arsenoplatin-1 C₄ H₈ As N₂ O₄ Pt OPINMBLEOXZNNE-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A]	T [auth A], U [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain T [auth A] Focus chain U [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]