5N27 | pdb_00005n27

X-ray structure of human heavy chain ferritin (apo form)

• PDB DOI: https://doi.org/10.2210/pdb5N27/pdb

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


• Deposited: 2017-02-07 Released: 2017-08-02 
• Deposition Author(s): Ferraro, G., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Cisplatin Binding Sites in Human H-Chain Ferritin.

Ferraro, G., Ciambellotti, S., Messori, L., Merlino, A.

(2017) Inorg Chem 56: 9064-9070

• PubMed: 28737381 
• DOI: https://doi.org/10.1021/acs.inorgchem.7b01072
• Primary Citation Related Structures: 
  5N26, 5N27


• PubMed Abstract: 
  

  The aim of this work is to identify the cisplatin binding sites on human H-chain ferritin. High-resolution X-ray crystallography reveals that cisplatin binds four distinct protein sites, that is, the side chains of His136 and Lys68, the side chain of His105, the side chain of Cys90 and the side chain of Cys102. These Pt binding sites are compared with those observed for the adduct that cisplatin forms upon encapsulation within horse spleen L-chain ferritin (87% identity with human L-chain ferritin).

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II , Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126 Naples, Italy.
Dipartimento di Chimica, Università di Firenze , Via Della Lastruccia 3, Sesto Fiorentino, 50019 Firenze, Italy.
Institute of Biostructures and Bioimages , Naples, Italy.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.53 kDa 
• Atom Count: 1,917 
• Modeled Residue Count: 174 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin heavy chain	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.955	α = 90
b = 182.955	β = 90
c = 182.955	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Ferraro, G., Merlino, A.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description