2iuk

Crystal structure of Soybean Lipoxygenase-D

Method: X-RAY DIFFRACTION

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

SEED LIPOXYGENASE

GLYCINE MAX

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LOXX_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–864； UniProt 1–864 Author chain B； PDBConstruct 1–864； UniProt 1–864

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	2iuk
Deposition date deposition_date	2006-06-05
Structure title title	Crystal structure of Soybean Lipoxygenase-D
Keywords keywords	;IRON, DIOXYGENASE, METAL-BINDING, OXIDOREDUCTASE, OXYLIPIN BIOSYNTHESIS, SOYBEAN LIPOXYGENASE-D, FATTY ACID BIOSYNTHESIS, LIPID SYNTHESIS ;; OXIDOREDUCTASE
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.

2iuk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2iuk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iuk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.11 Å
Rg (electron density)	28.36 Å
Total Rg	29.27 Å
Atom count	6649
Residues	834
Excluded volume	118880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iuk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2iuk__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 (3)

Entity 1 Entity 1 polymer

Description description	SEED LIPOXYGENASE
Molecular weight formula_weight	96867.8 kDa
EC 编号 ec_number	1.13.11.12
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	13534

MFGIFDKGQKIKGTVVLMPKNVLDFNAITSIGKGGVIDTATGILGQGVSLVGGVIDTATSFLGRNISMQLISATQTDGSGNGKVGKEVYLEKHLPTLPTLGARQDAFSIFFEWDASFGIPGAFYIKNFMTDEFFLVSVKLEDIPNHGTIEFVCNSWVYNFRSYKKNRIFFVNDTYLPSATPAPLLKYRKEEFEVLRGDGTGKRKDFDRIYDYDVYNDLGNPDGGDPRPILGGCSIYPYPLRVRTGRERTRTDPNSEKPGEVYVPRDENFGHLKSSDFLTYGIKSLSHDVIPLFKSAIFQLRVTSSEFESFEDVRSLYEGGIKLPTDILSQISPLPALKEIFRTDGENVLQFPPPHVAKVSKSGVMTDEEFAREVIAGVNPNVIRRLQEFPPKSTLDPTLYGDQTSTITKEQLEINMGGVTVEEALSTQRLFILDYQDAFIPYLTRINSLPTAKAYATRTILFLKDDGTLKPLAIELSKPHPDGDNLGPESIVVLPATEGVDSTIWLLAKAHVIVNDSGYHQLVSHWLNTHAVMEPFAIATNRHLSVLHPIYKLLYPHYRDTININGLARQSLINADGIIEKSFLPGKYSIEMSSSVYKNWVFTHQALPADLVKRGLAIEDPSAPHGLRLVIEDYPYAVDGLEIWDAIKTWVHEYVSLYYPTDAAVQQDTELQAWWKEAVEKGHGDLKEKPWWPKKQTTEDLIQSCSIIVWTASALHAAVNFGQYPYGGLILNRPTLARRFIPAEGTPEYDEMVKNPQKAYLRTITPKFETLIDLSVIEILSRHASDEIYLGERETPNWTTDKKALEAFKRFGSKLTGIEGKINARNSDPSLRNRTGPVQLPYTLLHRSSEEGLTFKGIPNSISI

Source Source

Source organism organism	GLYCINE MAX
Common name common_name	SOYBEAN
NCBI taxonomy ID ncbi_taxonomy_id	3847
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2iuka1
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.0 — automated matches

Domain ID domain_id	d2iuka2
Class class	a — All alpha proteins
Fold Fold fold	a.119 — Lipoxigenase
Superfamily Superfamily superfamily	a.119.1 — Lipoxigenase
Family Family family	a.119.1.1 — Plant lipoxigenases

Domain ID domain_id	d2iukb1
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.0 — automated matches

Domain ID domain_id	d2iukb2
Class class	a — All alpha proteins
Fold Fold fold	a.119 — Lipoxigenase
Superfamily Superfamily superfamily	a.119.1 — Lipoxigenase
Family Family family	a.119.1.1 — Plant lipoxigenases

CATH v4.4 (10 domains)

Domain ID domain_id	2iukA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	2iukA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	375 — Lipoxygenase-1; domain 2
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 2

Domain ID domain_id	2iukA03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	372 — Lipoxygenase-1; domain 3
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 3

Domain ID domain_id	2iukA04
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2iukA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	245 — Lipoxygenase-1; domain 5
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 5

Domain ID domain_id	2iukB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	2iukB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	375 — Lipoxygenase-1; domain 2
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 2

Domain ID domain_id	2iukB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	372 — Lipoxygenase-1; domain 3
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 3

Domain ID domain_id	2iukB04
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2iukB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	245 — Lipoxygenase-1; domain 5
Homologous superfamily homologous superfamily	10 — Lipoxygenase-1; Domain 5

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Unit-cell length a length_a	92.760 Å
Unit-cell length b length_b	115.100 Å
Unit-cell length c length_c	120.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.34 °
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	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	—

Crystal structure of Soybean Lipoxygenase-D

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

SEED LIPOXYGENASE

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

2iuk__assembly_2__model_1

2iuk__assembly_2__model_1 | I(q)

2iuk__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of Soybean Lipoxygenase-D

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

SEED LIPOXYGENASE

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

2iuk__assembly_2__model_1

2iuk__assembly_2__model_1 | I(q)

2iuk__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)