1gmn

CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR

Method: X-RAY DIFFRACTION Dmax: 68.6 Å Quality: GOOD

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

HEPATOCYTE GROWTH FACTOR

HOMO SAPIENS

UniProt P14210

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 28–210 Chain B; UniProt 28–210 Fragment:NK1 Mutation:YES ;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid ; × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;10% PEG8000, 8% ETHYLENE GLYCOL, 0.55M SODIUM DIHYDROGEN PHOSPHATE 0.10M SODIUM HEPES, PH 7.5 Resolution 2.30 Å R-free 0.279

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

35 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1gmn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gmn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1gmn
Deposition date deposition_date2001-09-19
Structure title titleCRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR
Keywords keywordsHGF/SF, HORMONE/GROWTH FACTOR, HORMONE-GROWTH FACTOR complex; HORMONE/GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.46
Radius of gyration Rg (electron density) rg_electron20.55
Forward intensity I(0) i020651800.00
Molecular weight molecular_weight32791.0 kDa
Excluded volume excluded_volume40301 ų
Envelope volume envelope_volume49006 ų
Hydration-shell volume shell_volume20350 ų
Envelope diameter envelope_diameter71.7
Shell Rg shell_rg26.49
Envelope Rg envelope_rg20.50
Shape Rg shape_rg20.52
Total Rg total_rg21.41
Total atoms total_atoms2286
Residues n_residues285
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.6
Rg (real space) rg_real21.39
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real2.0650e+07
I(0) uncertainty (real space) i0_real_error2.4610e+05
Rg (reciprocal space) rg_reciprocal21.40
I(0) (reciprocal space) i0_reciprocal20650000.0000
Solution quality estimate total_estimate0.8279
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.519
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4393000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1gmna1
Class classg — Small proteins
Fold Fold foldg.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamilyg.10.1 — Hairpin loop containing domain-like
Family Family familyg.10.1.1 — Hairpin loop containing domain
Domain ID domain_idd1gmna2
Class classg — Small proteins
Fold Fold foldg.14 — Kringle-like
Superfamily Superfamily superfamilyg.14.1 — Kringle-like
Family Family familyg.14.1.1 — Kringle modules
Domain ID domain_idd1gmnb1
Class classg — Small proteins
Fold Fold foldg.10 — Hairpin loop containing domain-like
Superfamily Superfamily superfamilyg.10.1 — Hairpin loop containing domain-like
Family Family familyg.10.1.1 — Hairpin loop containing domain
Domain ID domain_idd1gmnb2
Class classg — Small proteins
Fold Fold foldg.14 — Kringle-like
Superfamily Superfamily superfamilyg.14.1 — Kringle-like
Family Family familyg.14.1.1 — Kringle modules

CATH v4.4 (4 domains)

Domain ID domain_id1gmnA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily10 — Hepatocyte Growth Factor
Domain ID domain_id1gmnA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily10 — Plasminogen Kringle 4
Domain ID domain_id1gmnB01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology4 — Hepatocyte Growth Factor
Homologous superfamily homologous superfamily10 — Hepatocyte Growth Factor
Domain ID domain_id1gmnB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily10 — Plasminogen Kringle 4

8. Citations (1)

9. Files and Curves (10)