5cs3

The structure of the NK1 fragment of HGF/SF complexed with (H)EPPS

Method: X-RAY DIFFRACTION D_max: 69.6 Å Quality: REASONABLE

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

Hepatocyte growth factor

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–210 Chain B； UniProt 28–210	Fragment：UNP residues 28-210 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

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 5CS3	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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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
3HN4 Crystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor 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 monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–289（262 aa） 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
3MKP Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin Deposited 2010-04-15	Different mutation/modification 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 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 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 oligomeric state 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 oligomeric state 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 ligand/ion 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 ligand/ion 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 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
5CS5 The structure of the NK1 fragment of HGF/SF complexed with PIPES Deposited 2015-07-23	Different ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5cs3
Deposition date deposition_date	2015-07-23
Structure title title	The structure of the NK1 fragment of HGF/SF complexed with (H)EPPS
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

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

Radius of gyration Rg (Guinier) rg_guinier	21.78 Å
Radius of gyration Rg (electron density) rg_electron	21.07 Å
Forward intensity I(0) i0	28141500.00
Molecular weight molecular_weight	39818.0 kDa
Excluded volume excluded_volume	49617 Å³
Envelope volume envelope_volume	59803 Å³
Hydration-shell volume shell_volume	23567 Å³
Envelope diameter envelope_diameter	72.1 Å
Shell Rg shell_rg	27.53 Å
Envelope Rg envelope_rg	21.10 Å
Shape Rg shape_rg	21.08 Å
Total Rg total_rg	21.90 Å
Total atoms total_atoms	2790
Residues n_residues	346
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	69.6 Å
Rg (real space) rg_real	21.64 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.8140e+07
I(0) uncertainty (real space) i0_real_error	3.8270e+05
Rg (reciprocal space) rg_reciprocal	21.67 Å
I(0) (reciprocal space) i0_reciprocal	28140000.0000
Solution quality estimate total_estimate	0.7458
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.140
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8139000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 0.348; Positv: 1.000; Valcen: 1.000; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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	2889

YVEGQRKRRNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Komagataella pastoris CBS 7435

Entity 2 Entity 2 non-polymer

Description description	3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID
Molecular weight formula_weight	252.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5cs3a1
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	d5cs3a2
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	d5cs3b1
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	d5cs3b2
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	5cs3A01
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	5cs3A02
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	5cs3B01
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	5cs3B02
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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8. Citations (1)

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Unit-cell length a length_a	53.340 Å
Unit-cell length b length_b	63.378 Å
Unit-cell length c length_c	57.482 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.17 °
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	2.500 Å
Low-resolution limit resolution_low	34.300 Å
R factor r_factor	0.2180
R_work r_work	0.2130
R_free r_free	0.3180

fit	/app/data/saxs_computation/cs/5cs3/5cs3.fit
pddf	/app/data/pr_computation/cs/5cs3/5cs3.pr.out
profile	/app/data/saxs_computation/cs/5cs3/5cs3.dat