4iua

Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor

Method: X-RAY DIFFRACTION

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

Hepatocyte growth factor

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SULFATE ION × 2	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 4 SULFATE ION × 4	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SULFATE ION × 4	Consistent with protein count
12	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SULFATE ION × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SULFATE ION × 3	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SULFATE ION × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SULFATE ION × 3	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SULFATE ION × 3	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SULFATE ION × 2	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 SULFATE ION × 1	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SULFATE ION × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HGF_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–262； UniProt 31–290 Author chain B； PDBConstruct 3–262； UniProt 31–290 Author chain C； PDBConstruct 3–262； UniProt 31–290 Author chain D； PDBConstruct 3–262； UniProt 31–290 Author chain E； PDBConstruct 3–262； UniProt 31–290 Author chain F； PDBConstruct 3–262； UniProt 31–290 Author chain G； PDBConstruct 3–262； UniProt 31–290 Author chain H； PDBConstruct 3–262； UniProt 31–290

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	4iua
Deposition date deposition_date	2013-01-20
Structure title title	Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor
Keywords keywords	HGF/SF, HORMONE, KRINGLE domain, GROWTH FACTOR; HORMONE
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.

4iua__assembly_2__model_1

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

Download this curve (.dat)

4iua__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4iua__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.67 Å
Rg (electron density)	20.05 Å
Total Rg	20.87 Å
Atom count	2113
Residues	254
Excluded volume	36981 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4iua__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4iua__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4iua__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4iua__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4iua__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4iua__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4iua__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4iua__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4iua__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4iua__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4iua__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4iua__assembly_12__model_1`	dimeric （2）	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	Hepatocyte growth factor
Molecular weight formula_weight	30414.3 kDa
Mutation mutation	C215A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	16628

GSEGQKKRRNTLHEFKKSAKTTLTKEDPLLKIKTKKVNSADECANRCIRNRGFTFTCKAFVFDKSRKRCYWYPFNSMSSGVKKGFGHEFDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWNSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVECMTANGESYRGPMDHTESGKTCQRWDQQTPHRHKFLPERYPDKGFDDNYCRNPDGKPRPWCYTLDPDTPWEYCAIKTCA

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d4iuaa1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuaa2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuaa3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuab1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuab2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuab3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuac1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuac2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuac3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuad1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuad2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuad3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuae1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuae2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuae3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuaf1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuaf2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuaf3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuag1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuag2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuag3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuah1
Class class	g — Small proteins
Fold Fold fold	g.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamily	g.10.1 — Hairpin loop containing domain-like
Family Family family	g.10.1.1 — Hairpin loop containing domain

Domain ID domain_id	d4iuah2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d4iuah3
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

CATH v4.4 (24 domains)

Domain ID domain_id	4iuaA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaC01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaC03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaD01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaE01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaE03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaF01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaF03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaG01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaG02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaG03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaH01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily	10 — Hepatocyte Growth Factor

Domain ID domain_id	4iuaH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	4iuaH03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

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Unit-cell length a length_a	92.620 Å
Unit-cell length b length_b	127.328 Å
Unit-cell length c length_c	129.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	29.775 Å
R factor r_factor	0.1829
R_work r_work	0.1758
R_free r_free	0.2452

Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor

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

Hepatocyte growth factor

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

4iua__assembly_2__model_1

4iua__assembly_2__model_1 | I(q)

4iua__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 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal Structure of the NK2 Fragment (31-290) of the mouse Hepatocyte Growth Factor/Scatter Factor

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

Hepatocyte growth factor

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

4iua__assembly_2__model_1

4iua__assembly_2__model_1 | I(q)

4iua__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 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)