9lny

Crystal structure of human heavy chain Ferritin binding with dinitrosyl iron complex modificated by phenylboronic acid

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferritin heavy chain, N-terminally processed

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 24	FE (III) ION × 96 MAGNESIUM ION × 72 CHLORIDE ION × 72 NITRIC OXIDE × 48 [3-(bromomethyl)phenyl]boronic acid × 24 HYDROSULFURIC ACID × 24 water × 24	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 24	FE (III) ION × 96 MAGNESIUM ION × 72 CHLORIDE ION × 72 NITRIC OXIDE × 48 [3-(bromomethyl)phenyl]boronic acid × 24 HYDROSULFURIC ACID × 24 water × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FRIH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–172； UniProt 6–177

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9lny
Deposition date deposition_date	2025-01-22
Last revision last_revision	2025-11-26
Structure title title	Crystal structure of human heavy chain Ferritin binding with dinitrosyl iron complex modificated by phenylboronic acid
Keywords keywords	Human Ferritin, METAL BINDING PROTEIN, Iron Sulfur Cluster; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9lny__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9lny__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lny__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	55.14 Å
Rg (electron density)	54.05 Å
Total Rg	54.42 Å
Atom count	34252
Residues	4104
Excluded volume	602870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lny__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9lny__assembly_2__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Ferritin heavy chain, N-terminally processed
Molecular weight formula_weight	20116.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1568

TSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWESGLNAMECALHLEKNVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	NITRIC OXIDE
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	[3-(bromomethyl)phenyl]boronic acid
Molecular weight formula_weight	214.9 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	HYDROSULFURIC ACID
Molecular weight formula_weight	34.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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Unit-cell length a length_a	187.262 Å
Unit-cell length b length_b	187.262 Å
Unit-cell length c length_c	187.262 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	96

Space group space_group	F 4 3 2
Space-group number int_tables_number	209
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	46.815 Å
R factor r_factor	0.1900
R_work r_work	0.1870
R_free r_free	0.2424

Crystal structure of human heavy chain Ferritin binding with dinitrosyl iron complex modificated by phenylboronic acid

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferritin heavy chain, N-terminally processed

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lny__assembly_1__model_1

9lny__assembly_1__model_1 | I(q)

9lny__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of human heavy chain Ferritin binding with dinitrosyl iron complex modificated by phenylboronic acid

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ferritin heavy chain, N-terminally processed

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lny__assembly_1__model_1

9lny__assembly_1__model_1 | I(q)

9lny__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)