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3hn4

Crystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor

Method: X-RAY DIFFRACTION Dmax: 68.9 Å Quality: GOOD
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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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 28–289 Fragment：UNP residues 28-289 Mutation：K132E, R134E, C214A EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；50 mM Ammonium sulfate, 17-23% PEG 2000 or 4000, 100 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, 0.5 mM Beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.60 Å R-free 0.333

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.

Other PDB Difference from Current Entry 3HN4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BHT NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR Deposited 1998-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 35–210（176 aa） Fragment：NK1 FRAGMENT, HEPARIN BINDING DOMAIN PLUS C-MET BINDING DOMAIN
Chain B 35–210（176 aa） Fragment：NK1 FRAGMENT, HEPARIN BINDING DOMAIN PLUS C-MET BINDING DOMAIN
Not recorded SO4 SULFATE ION × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；40% PEG 3400, 0.1M HEPES PH 7.5, 0.3M AMMONIUM SULFATE. PROTEIN CONCENTRATION OF 3MG/ML
Resolution 2.00 Å R-free 0.247
1GMN CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR Deposited 2001-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：NK1
Chain B 28–210（183 aa） Fragment：NK1
Mutation：YES Mutation：YES 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
1GMO CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR Deposited 2001-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：NK1
Chain B 28–210（183 aa） Fragment：NK1
Mutation：YES Mutation：YES SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；10% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5
Resolution 3.00 Å R-free 0.295
1GMO CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR Deposited 2001-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 28–210（183 aa） Fragment：NK1
Chain D 28–210（183 aa） Fragment：NK1
Mutation：YES Mutation：YES SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；10% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5
Resolution 3.00 Å R-free 0.295
1GMO CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR Deposited 2001-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 28–210（183 aa） Fragment：NK1
Chain F 28–210（183 aa） Fragment：NK1
Mutation：YES Mutation：YES SO4 SULFATE ION × 3 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；10% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5
Resolution 3.00 Å R-free 0.295
1GMO CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR Deposited 2001-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 28–210（183 aa） Fragment：NK1
Chain H 28–210（183 aa） Fragment：NK1
Mutation：YES Mutation：YES SO4 SULFATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；10% PEG4000, 8% ETHYLENE GLYCOL, 0.10M SODIUM PARA-TOLUENE SULFONATE,0.10M SODIUM HEPES, PH 7.5
Resolution 3.00 Å R-free 0.295
1GP9 A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping Deposited 2001-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 40–210（171 aa） Fragment：NK1, RESIDUES 40-210
Chain B 40–210（171 aa） Fragment：NK1, RESIDUES 40-210
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；18% PEG4000, 10% 2-PROPANOL, 0.1M SODIUM HEPES, PH 7.5
Resolution 2.50 Å R-free 0.288
1GP9 A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping Deposited 2001-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 40–210（171 aa） Fragment：NK1, RESIDUES 40-210
Chain D 40–210（171 aa） Fragment：NK1, RESIDUES 40-210
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；18% PEG4000, 10% 2-PROPANOL, 0.1M SODIUM HEPES, PH 7.5
Resolution 2.50 Å R-free 0.288
1NK1 NK1 FRAGMENT OF HUMAN HEPATOCYTE GROWTH FACTOR/SCATTER FACTOR (HGF/SF) AT 2.5 ANGSTROM RESOLUTION Deposited 1998-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：NK1
Chain B 28–210（183 aa） Fragment：NK1
Mutation：A29V Mutation：A29V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.7；18% PEG4000, 0.20M SODIUM ACETATE, 0.15M TRIS, PH 8.5 , pH 8.7
Resolution 2.50 Å R-free 0.319
1SHY The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor. Deposited 2004-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 495–728（234 aa） Fragment：HGF beta chain
Mutation：C604S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 3.22 Å R-free 0.270
1SI5 Protease-like domain from 2-chain hepatocyte growth factor Deposited 2004-02-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 495–728（234 aa） Fragment：protease-like domain
Mutation：Cys604Ser No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；NaCl, CaCl2, PEG 1500, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.53 Å R-free 0.301
2HGF HAIRPIN LOOP CONTAINING DOMAIN OF HEPATOCYTE GROWTH FACTOR, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–127（97 aa） Fragment：AMINO TERMINAL DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；303 K
Resolution not provided
2QJ2 A Mechanistic Basis for Converting a Receptor Tyrosine Kinase Agonist to an Antagonist Deposited 2007-07-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–209（182 aa） Fragment：residues 28-209
Chain B 28–209（182 aa） Fragment：residues 28-209
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；50 mM ammonium sulfate, 26-29% PEG 4000 (w/w), 100 mM Tris-HCl pH 8.0, 0.5 mM beta-octyl glucoside, and 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.81 Å R-free 0.248
3HMS Crystal Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, orthorhombic crystal form Deposited 2009-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–126（99 aa） Fragment：N-terminal domain: UNP residues 28-126
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；50 mM Ammonium sulfate, 28-32% PEG 1000 or 2000, 50 mM Tris-HCl pH 8.0, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.255
3HMT Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, trigonal crystal form Deposited 2009-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–126（99 aa） Fragment：N-terminal domain: UNP residues 28-126
Chain B 28–126（99 aa） Fragment：N-terminal domain: UNP residues 28-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
3HMT Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, trigonal crystal form Deposited 2009-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–126（99 aa） Fragment：N-terminal domain: UNP residues 28-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
3HMT Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, trigonal crystal form Deposited 2009-05-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–126（99 aa） Fragment：N-terminal domain: UNP residues 28-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.243
3MKP Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin Deposited 2010-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：K132E, R134E Mutation：K132E, R134E SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 SGN 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K
Resolution 2.81 Å R-free 0.261
3MKP Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin Deposited 2010-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 28–210（183 aa） Fragment：UNP residues 28-210
Chain D 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：K132E, R134E Mutation：K132E, R134E SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K
Resolution 2.81 Å R-free 0.261
3SP8 Crystal structure of NK2 in complex with fractionated Heparin DP10 Deposited 2011-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–288（261 aa） Fragment：NK2
Chain B 28–288（261 aa） Fragment：NK2
Mutation：G146D, C214S Mutation：G146D, C214S MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；50mM MES pH=6.0, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 21K, temperature 294K
Resolution 1.86 Å R-free 0.217
3SP8 Crystal structure of NK2 in complex with fractionated Heparin DP10 Deposited 2011-07-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–288（261 aa） Fragment：NK2
Mutation：G146D, C214S MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；50mM MES pH=6.0, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 21K, temperature 294K
Resolution 1.86 Å R-free 0.217
3SP8 Crystal structure of NK2 in complex with fractionated Heparin DP10 Deposited 2011-07-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–288（261 aa） Fragment：NK2
Mutation：G146D, C214S MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；50mM MES pH=6.0, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 21K, temperature 294K
Resolution 1.86 Å R-free 0.217
4D3C Crystal structure of the NK1 domain of HGF in complex with anti-HGF monoclonal antibody SFN68. Deposited 2014-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 32–210（179 aa） Fragment：RESIDUES 23-210
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.62 Å R-free 0.298
4K3J Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta Deposited 2013-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 495–721（227 aa） Fragment：unp residues 495-721
Mutation：C604S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；0.1 M sodium cacodylate pH 6.2, 20% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.80 Å R-free 0.253
4O3T Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP.14 Deposited 2013-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 495–728（234 aa） Fragment：HGF-beta (UNP Residues 25-567)
Mutation：V495G/C604S 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG6000, 800 mM NaCl, 400 mM trimethylammonium oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.99 Å R-free 0.276
4O3U Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP2.3 Deposited 2013-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 495–728（234 aa） Fragment：HGF-beta (UNP Residues 25-567)
Mutation：V495G/C604S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；8% PEG8000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.04 Å R-free 0.251
5COE The structure of the NK1 fragment of HGF/SF complexed with HEPES Deposited 2015-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 2.18 Å R-free 0.264
5CP9 The structure of the NK1 fragment of HGF/SF complexed with MB605 Deposited 2015-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V 6O5 3-(furan-2-yl)propanoic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 1.90 Å R-free 0.227
5CS1 The structure of the NK1 fragment of HGF/SF Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 nM Na Acetate, 150 mM Tris
Resolution 2.00 Å R-free 0.255
5CS3 The structure of the NK1 fragment of HGF/SF complexed with (H)EPPS Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V EP1 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 2.50 Å R-free 0.318
5CS5 The structure of the NK1 fragment of HGF/SF complexed with PIPES Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V PIN PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 1.90 Å R-free 0.240
5CS9 The structure of the NK1 fragment of HGF/SF complexed with MES Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000. 200 mM Na Acetate, 150 mM Tris
Resolution 2.00 Å R-free 0.251
5CSQ The structure of the NK1 fragment of HGF/SF complexed with MOPS Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM NA Acetate, 150 mM Tris
Resolution 1.95 Å R-free 0.274
5CT1 The structure of the NK1 fragment of HGF/SF complexed with CHES Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 2.00 Å R-free 0.269
5CT2 The structure of the NK1 fragment of HGF/SF complexed with CAPS Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 2.00 Å R-free 0.295
5CT3 The structure of the NK1 fragment of HGF/SF complexed with 2FA Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–210（183 aa） Fragment：UNP residues 28-210
Chain B 28–210（183 aa） Fragment：UNP residues 28-210
Mutation：A29V Mutation：A29V 54O 3-hydroxypropane-1-sulfonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Resolution 2.00 Å R-free 0.251
6LZ9 t8E4 antibody Fab complexed with the active form of HGF Deposited 2020-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 388–494（107 aa） Fragment：K4 domain
Chain B 495–728（234 aa） Fragment：SP domain
Mutation：N402Q, T476G, K491I, Q492E, L493G Mutation：C561S, N566Q, N653Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10 % (w/v) PEG 10000, 0.1M Magnesium acetate, 0.1M MES pH 6.5
Resolution 2.80 Å R-free 0.297
7MO7 Cryo-EM structure of 2:2 c-MET/HGF holo-complex Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–728（728 aa）
Chain D 1–728（728 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7MO8 Cryo-EM structure of 1:1 c-MET I/HGF I complex after focused 3D refinement of holo-complex Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–728（728 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7MO9 Cryo-EM map of the c-MET II/HGF I/HGF II (K4 and SPH) sub-complex Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–728（728 aa）
Chain D 1–728（728 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7MOA Cryo-EM structure of the c-MET II/HGF I complex bound with HGF II in a rigid conformation Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–728（728 aa）
Chain D 1–728（728 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7MOB Cryo-EM structure of 2:2 c-MET/NK1 complex Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–210（210 aa）
Chain B 1–210（210 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7OCL K1K1, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic Deposited 2021-04-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 125–211（87 aa）
Chain A 129–210（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290.15 K；100 mM Tris/Bicine pH 8.5, 30 mM Sodium nitrate, 30 mM Sodium phosphate dibasic, 30 mM Ammonium sulfate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
Resolution 1.80 Å R-free 0.227
7OCL K1K1, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic Deposited 2021-04-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 125–211（87 aa）
Chain B 129–210（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290.15 K；100 mM Tris/Bicine pH 8.5, 30 mM Sodium nitrate, 30 mM Sodium phosphate dibasic, 30 mM Ammonium sulfate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
Resolution 1.80 Å R-free 0.227
7OCM K1K1H6, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic Deposited 2021-04-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 125–211（87 aa）
Chain A 129–210（82 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290.15 K；100 mM MOPS/HEPES pH 7.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 20% v/v glycerol, 10% w/v PEG4000
Resolution 1.70 Å R-free 0.195

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 3–264； UniProt 28–289

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 3hn4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3hn4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3hn4
Deposition date deposition_date2009-05-29
Structure title titleCrystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor
Keywords keywordsHGF/SF, hormone/growth factor, Disulfide bond, Glycoprotein, Growth factor, Kringle, Serine protease homolog, HORMONE; HORMONE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.57 Å
Radius of gyration Rg (electron density) rg_electron19.95 Å
Forward intensity I(0) i017904000.00
Molecular weight molecular_weight30468.0 kDa
Excluded volume excluded_volume37466 ų
Envelope volume envelope_volume45058 ų
Hydration-shell volume shell_volume19205 ų
Envelope diameter envelope_diameter70.4 Å
Shell Rg shell_rg25.73 Å
Envelope Rg envelope_rg20.03 Å
Shape Rg shape_rg19.95 Å
Total Rg total_rg20.75 Å
Total atoms total_atoms2130
Residues n_residues256
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.9 Å
Rg (real space) rg_real20.51 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real1.7900e+07
I(0) uncertainty (real space) i0_real_error2.1800e+05
Rg (reciprocal space) rg_reciprocal20.53 Å
I(0) (reciprocal space) i0_reciprocal17900000.0000
Solution quality estimate total_estimate0.8921
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9 Å
Skewness Skewness skewness0.226
Kurtosis Kurtosis kurtosis-0.475
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4404000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.996
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3hn4a1
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_idd3hn4a2
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_idd3hn4a3
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 (3 domains)

Domain ID domain_id3hn4A01
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_id3hn4A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily10 — Plasminogen Kringle 4
Domain ID domain_id3hn4A03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily10 — Plasminogen Kringle 4
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8. Citations (1)

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9. Files and Curves (10)