2b3y

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)

Method: X-RAY DIFFRACTION

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

Iron-responsive element binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 1 IRON/SULFUR CLUSTER × 1 GLYCEROL × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 IRON/SULFUR CLUSTER × 1 FORMIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IREB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–888； UniProt 2–889 Author chain B； PDBConstruct 1–888； UniProt 2–889

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	2b3y
Deposition date deposition_date	2005-09-22
Structure title title	Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)
Keywords keywords	IRP1 IRE-IRP1 aconitase activity, LYASE; LYASE
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.

2b3y__assembly_1__model_1

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

Download this curve (.dat)

2b3y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2b3y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.88 Å
Rg (electron density)	26.88 Å
Total Rg	27.66 Å
Atom count	6952
Residues	888
Excluded volume	124390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b3y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2b3y__assembly_2__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Iron-responsive element binding protein 1
Molecular weight formula_weight	98374.4 kDa
EC 编号 ec_number	4.2.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14870

SNPFAHLAEPLDPVQPGKKFFNLNKLEDSRYGRLPFSIRVLLEAAIRNCDEFLVKKQDIENILHWNVTQHKNIEVPFKPARVILQDFTGVPAVVDFAAMRDAVKKLGGDPEKINPVCPADLVIDHSIQVDFNRRADSLQKNQDLEFERNRERFEFLKWGSQAFHNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGILGWGVGGIEAEAVMLGQPISMVLPQVIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATAAFFPVDEVSITYLVQTGRDEEKLKYIKKYLQAVGMFRDFNDPSQDPDFTQVVELDLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPEHHNDHKTFIYDNTEFTLAHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVDAGLNVMPYIKTSLSPGSGVVTYYLQESGVMPYLSQLGFDVVGYGCMTCIGNSGPLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGVNAKGQQVFLKDIWPTRDEIQAVERQYVIPGMFKEVYQKIETVNESWNALATPSDKLFFWNSKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAVMARGTFANIRLLNRFLNKQAPQTIHLPSGEILDVFDAAERYQQAGLPLIVLAGKEYGAGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADALGLTGQERYTIIIPENLKPQMKVQVKLDTGKTFQAVMRFDTDVELTYFLNGGILNYMIRKMAK

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	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	970

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2b3ya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.2 — LeuD/IlvD-like
Family Family family	c.8.2.1 — LeuD-like

Domain ID domain_id	d2b3ya2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.83 — Aconitase iron-sulfur domain
Superfamily Superfamily superfamily	c.83.1 — Aconitase iron-sulfur domain
Family Family family	c.83.1.1 — Aconitase iron-sulfur domain

Domain ID domain_id	d2b3yb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.2 — LeuD/IlvD-like
Family Family family	c.8.2.1 — LeuD-like

Domain ID domain_id	d2b3yb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.83 — Aconitase iron-sulfur domain
Superfamily Superfamily superfamily	c.83.1 — Aconitase iron-sulfur domain
Family Family family	c.83.1.1 — Aconitase iron-sulfur domain

CATH v4.4 (10 domains)

Domain ID domain_id	2b3yA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	2b3yA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1060 — Aconitase; Domain 2
Homologous superfamily homologous superfamily	10 — Aconitase, Domain 2

Domain ID domain_id	2b3yA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	2b3yA04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	190 — Apolipoprotein Cii; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2b3yA05
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	19 — Aconitase; domain 4
Homologous superfamily homologous superfamily	10 — Aconitase, domain 4

Domain ID domain_id	2b3yB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	2b3yB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1060 — Aconitase; Domain 2
Homologous superfamily homologous superfamily	10 — Aconitase, Domain 2

Domain ID domain_id	2b3yB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	2b3yB04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	190 — Apolipoprotein Cii; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2b3yB05
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	19 — Aconitase; domain 4
Homologous superfamily homologous superfamily	10 — Aconitase, domain 4

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Unit-cell length a length_a	63.910 Å
Unit-cell length b length_b	215.470 Å
Unit-cell length c length_c	64.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	72.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	29.500 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2610

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)

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

Iron-responsive element binding protein 1

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

2b3y__assembly_1__model_1

2b3y__assembly_1__model_1 | I(q)

2b3y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (2)

Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)

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

Iron-responsive element binding protein 1

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

2b3y__assembly_1__model_1

2b3y__assembly_1__model_1 | I(q)

2b3y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (2)