8KFD

Ferritin drug carrier(FDC) for encapsulated platinum (IV) prodrug for esophageal squamous cell carcinoma targeted therapy

PDB DOI: https://doi.org/10.2210/pdb8KFD/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-05-29
Deposition Author(s): Chen, X.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.166
R-Value Work: 0.153
R-Value Observed: 0.154

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Ferritin drug carrier(FDC) for encapsulated platinum (IV) prodrug for esophageal squamous cell carcinoma targeted therapy

Jiang, B., Chen, X., Fan, K.

To be published.

Macromolecule Content

Total Structure Weight: 22.13 kDa
Atom Count: 1,843
Modelled Residue Count: 172
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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): 0 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT (Subject of Investigation/LOI) Query on PT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions 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] Interactions & Density 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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A]	S [auth A], T [auth A], U [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.166
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.45	α = 90
b = 183.45	β = 90
c = 183.45	γ = 90

Software Package:

Software Name	Purpose
DIALS	data collection
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-29

Deposition Author(s):

Chen, X.

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC2102900
Ministry of Science and Technology (MoST, China)	China	2021YFA1201102
National Natural Science Foundation of China (NSFC)	China	32000996