6kbr

Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex

Method: X-RAY DIFFRACTION D_max: 60.0 Å Quality: GOOD

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

Kallikrein-4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–254	Not recorded	K41043 × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；Lithium chloride, polyethylene glycol 3350	Resolution 2.00 Å R-free 0.226

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 6KBR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BDG Human Kallikrein 4 complex with nickel and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 1 NI NICKEL (II) ION × 2 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG-MME 2000, 100 mM Tris, 10 mM nickel chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.225
2BDG Human Kallikrein 4 complex with nickel and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	CL CHLORIDE ION × 1 NI NICKEL (II) ION × 2 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG-MME 2000, 100 mM Tris, 10 mM nickel chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.225
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	ZN ZINC ION × 1 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulphate, 100 mM HEPES, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.292
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulphate, 100 mM HEPES, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.292
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulphate, 100 mM HEPES, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.292
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulphate, 100 mM HEPES, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.292
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–45（19 aa） Fragment：Human Kallikrein 4 Chain B 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	ZN ZINC ION × 1 PBZ P-AMINO BENZAMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.6 M ammonium sulphate, 100 mM HEPES, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.292
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	CO COBALT (II) ION × 1 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain K 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain L 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain M 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	CO COBALT (II) ION × 1 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain N 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain O 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain P 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct 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 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	CO COBALT (II) ION × 1 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
2BDI Human Kallikrein 4 complex with cobalt and p-aminobenzamidine Deposited 2005-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain I 27–45（19 aa） Fragment：Human Kallikrein 4	Not recorded	CO COBALT (II) ION × 1 PBZ P-AMINO BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.296
4K1E Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR Deposited 2013-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–253（223 aa） Fragment：Related Peptidase 4, UNP residues 31-253	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 LI LITHIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M lithium sulfate, 0.1M sodium acetate, 30% PEG 8000 , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.30 Å R-free 0.170
4K8Y Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with Sunflower Trypsin Inhibitor (SFTI-1) Deposited 2013-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–253（223 aa） Fragment：Related Peptidase 4, UNP residues 31-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 20%(w/v) PEG 8000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.00 Å R-free 0.170
4KEL Atomic resolution crystal structure of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR(N) Deposited 2013-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 31–253（223 aa） Fragment：Related Peptidase 4, UNP residues 31-253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M lithium sulfate, 0.1M sodium acetate, 30% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.15 Å R-free 0.163
4KGA Crystal structure of kallikrein-related peptidase 4 Deposited 2013-04-29	Different construct 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 31–253（223 aa） Fragment：Related Peptidase 4, UNP residues 31-253	Not recorded	NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM NiCl2, 100mM Tris, 20% PEG2000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.32 Å R-free 0.264
4KGA Crystal structure of kallikrein-related peptidase 4 Deposited 2013-04-29	Different construct 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 31–253（223 aa） Fragment：Related Peptidase 4, UNP residues 31-253	Not recorded	NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10mM NiCl2, 100mM Tris, 20% PEG2000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.32 Å R-free 0.264
6NVB Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 Deposited 2019-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–254（224 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000 cryoprotectant = 1:1 glycerol : mother liquor	Resolution 1.64 Å R-free 0.180
6NVB Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 Deposited 2019-02-04	Different construct 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 31–254（224 aa）	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000 cryoprotectant = 1:1 glycerol : mother liquor	Resolution 1.64 Å R-free 0.180
6NVB Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 Deposited 2019-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 31–254（224 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000 cryoprotectant = 1:1 glycerol : mother liquor	Resolution 1.64 Å R-free 0.180
6NVB Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 Deposited 2019-02-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 31–254（224 aa）	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000 cryoprotectant = 1:1 glycerol : mother liquor	Resolution 1.64 Å R-free 0.180
7JQK Crystal structure of the R64A mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 31–253（223 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	2PE NONAETHYLENE GLYCOL × 2 CD CADMIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2.0M Ammonium Sulfate 2% PEG400, 10mM CdCl2 at pH 7.5	Resolution 1.33 Å R-free 0.153
7JQN Crystal structure of the R64M mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 31–253（223 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	2PE NONAETHYLENE GLYCOL × 3 CD CADMIUM ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2.0 Ammonium Sulfate, 2%PEG400, 10mM CdCl2 pH 7.5	Resolution 1.50 Å R-free 0.161
7JQO Crystal structure of the R64D mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 Deposited 2020-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 31–253（223 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	2PE NONAETHYLENE GLYCOL × 3 CD CADMIUM ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0M Ammounium Sulfate, 2% PEG400, 10mM CdCl2	Resolution 1.60 Å R-free 0.152

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

View Construct and Data Evidence

UniProt name	KLK4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254

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	6kbr
Deposition date deposition_date	2019-06-26
Structure title title	Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex
Keywords keywords	;Protein engineering, Cystine knot protein, Protease inhibitor, Structural analysis, PROTEIN BINDING, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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	18.85 Å
Radius of gyration Rg (electron density) rg_electron	17.77 Å
Forward intensity I(0) i0	17277100.00
Molecular weight molecular_weight	29904.0 kDa
Excluded volume excluded_volume	36773 Å³
Envelope volume envelope_volume	42155 Å³
Hydration-shell volume shell_volume	19425 Å³
Envelope diameter envelope_diameter	59.6 Å
Shell Rg shell_rg	24.54 Å
Envelope Rg envelope_rg	18.14 Å
Shape Rg shape_rg	17.76 Å
Total Rg total_rg	18.71 Å
Total atoms total_atoms	2083
Residues n_residues	278
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	60.0 Å
Rg (real space) rg_real	18.73 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.7280e+07
I(0) uncertainty (real space) i0_real_error	2.1110e+05
Rg (reciprocal space) rg_reciprocal	18.75 Å
I(0) (reciprocal space) i0_reciprocal	17280000.0000
Solution quality estimate total_estimate	0.8917
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.168
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4227000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Kallikrein-4
Molecular weight formula_weight	27048.6 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2193

MATAGNPWGWFLGYLILGVAGSLVSGSCSQIINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGHDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQAS

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	K41043
Molecular weight formula_weight	7259.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PQFGLFSKYRTPNCRRYSIHGCNRMYAPVCGSDMSTYANECTLCMKIREGGHNIKIIKNGPCGAS

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	Origami vector p7308

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	110

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6kbrc_
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	6kbrA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6kbrA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6kbrC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	145.208 Å
Unit-cell length b length_b	41.620 Å
Unit-cell length c length_c	43.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	72.577 Å
R factor r_factor	0.1875
R_work r_work	0.1854
R_free r_free	0.2258

fit	/app/data/saxs_computation/kb/6kbr/6kbr.fit
pddf	/app/data/pr_computation/kb/6kbr/6kbr.pr.out
profile	/app/data/saxs_computation/kb/6kbr/6kbr.dat

Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex

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

Kallikrein-4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)