SAXSdb — 5cp9

▼

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

Hepatocyte growth factor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3-(furan-2-yl)propanoic acid × 1 1,2-ETHANEDIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HGF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 28–210 Author chain B； PDBConstruct 1–183； UniProt 28–210

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	5cp9
Deposition date deposition_date	2015-07-21
Structure title title	The structure of the NK1 fragment of HGF/SF complexed with MB605
Keywords keywords	HGF/SF, NK1 fragment, fragment based drug discovery, growth factor, cell cycle, hormone, new chemical entity; HORMONE
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.

5cp9__assembly_1__model_1

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

Download this curve (.dat)

5cp9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cp9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.74 Å
Rg (electron density)	21.05 Å
Total Rg	21.86 Å
Atom count	2788
Residues	346
Excluded volume	49572 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cp9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Hepatocyte growth factor
Molecular weight formula_weight	21172.3 kDa
Mutation mutation	A29V
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	3028

YVEGQRKRRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Komagataella pastoris CBS 7435

Entity 2 Entity 2 non-polymer

Description description	3-(furan-2-yl)propanoic acid
Molecular weight formula_weight	140.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

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

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5cp9a1
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	d5cp9a2
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	d5cp9b1
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	d5cp9b2
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 (4 domains)

Domain ID domain_id	5cp9A01
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	5cp9A02
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	5cp9B01
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	5cp9B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

▶

Unit-cell length a length_a	53.387 Å
Unit-cell length b length_b	63.649 Å
Unit-cell length c length_c	57.198 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.24 °
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	1.900 Å
Low-resolution limit resolution_low	26.580 Å
R factor r_factor	0.1960
R_work r_work	0.1950
R_free r_free	0.2270

The structure of the NK1 fragment of HGF/SF complexed with MB605

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

5cp9__assembly_1__model_1

5cp9__assembly_1__model_1 | I(q)

5cp9__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

The structure of the NK1 fragment of HGF/SF complexed with MB605

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

5cp9__assembly_1__model_1

5cp9__assembly_1__model_1 | I(q)

5cp9__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)