SAXSdb — 1fhf

▼

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

SEED COAT PEROXIDASE

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	CALCIUM ION × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O22443_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–304； UniProt 27–330 Author chain B； PDBConstruct 1–304； UniProt 27–330 Author chain C； PDBConstruct 1–304； UniProt 27–330

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1fhf
Deposition date deposition_date	2000-08-01
Structure title title	THE STRUCTURE OF SOYBEAN PEROXIDASE
Keywords keywords	OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1fhf__assembly_1__model_1

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

Download this curve (.dat)

1fhf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1fhf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.52 Å
Rg (electron density)	19.48 Å
Total Rg	20.31 Å
Atom count	2390
Residues	304
Excluded volume	42273 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1fhf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1fhf__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1fhf__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SEED COAT PEROXIDASE
Molecular weight formula_weight	33138.0 kDa
EC 编号 ec_number	1.11.1.7
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7182

QLTPTFYRETCPNLFPIVFGVIFDASFTDPRIGASLMRLHFHDCFVQGCDGSVLLNNTDTIESEQDALPNINSIRGLDVVNDIKTAVENSCPDTVSCADILAIAAEIASVLGGGPGWPVPLGRRDSLTANRTLANQNLPAPFFNLTQLKASFAVQGLNTLDLVTLSGGHTFGRARCSTFINRLYNFSNTGNPDPTLNTTYLEVLRARCPQNATGDNLTNLDLSTPDQFDNRYYSNLLQLNGLLQSDQELFSTPGADTIPIVNSFSSNQNTFFSNFRVSMIKMGNIGVLTGDEGEIRLQCNFVNG

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

▼

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1fhfa_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

Domain ID domain_id	d1fhfb_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

Domain ID domain_id	d1fhfc_
Class class	a — All alpha proteins
Fold Fold fold	a.93 — Heme-dependent peroxidases
Superfamily Superfamily superfamily	a.93.1 — Heme-dependent peroxidases
Family Family family	a.93.1.1 — CCP-like

CATH v4.4 (6 domains)

Domain ID domain_id	1fhfA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1fhfA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	1fhfB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1fhfB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

Domain ID domain_id	1fhfC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1fhfC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	420 — Peroxidase; domain 2
Homologous superfamily homologous superfamily	10 — Peroxidase, domain 2

▶

Unit-cell length a length_a	106.454 Å
Unit-cell length b length_b	106.454 Å
Unit-cell length c length_c	104.996 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	11.000 Å
R factor r_factor	0.2710
R_work r_work	0.2710
R_free r_free	0.2890

THE STRUCTURE OF SOYBEAN PEROXIDASE

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

SEED COAT PEROXIDASE

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

1fhf__assembly_1__model_1

1fhf__assembly_1__model_1 | I(q)

1fhf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

THE STRUCTURE OF SOYBEAN PEROXIDASE

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

SEED COAT PEROXIDASE

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

1fhf__assembly_1__model_1

1fhf__assembly_1__model_1 | I(q)

1fhf__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)