2bdg

Human Kallikrein 4 complex with nickel and p-aminobenzamidine

Method: X-RAY DIFFRACTION D_max: 84.8 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 27–45	Fragment：Human Kallikrein 4	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 27–45	Fragment：Human Kallikrein 4	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

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 2BDG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BDH Human Kallikrein 4 complex with zinc and p-aminobenzamidine Deposited 2005-10-20	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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
6KBR Crystal structure of Human KLK4 and SPINK2 derived KLK4 inhibitor complex Deposited 2019-06-26	Different construct 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 1–254（254 aa）	Not recorded	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
6NVB Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 Deposited 2019-02-04	Different construct Different ligand/ion 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 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 ligand/ion 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 34 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 1–217； UniProt 27–45 Author chain B； PDBConstruct 1–217； UniProt 27–45

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	2bdg
Deposition date deposition_date	2005-10-20
Structure title title	Human Kallikrein 4 complex with nickel and p-aminobenzamidine
Keywords keywords	serine proteinase, s1 subsite, 70-80 loop, Structural Proteomics in Europe, SPINE, Structural Genomics, Hydrolase; HYDROLASE
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	26.15 Å
Radius of gyration Rg (electron density) rg_electron	25.16 Å
Forward intensity I(0) i0	42483300.00
Molecular weight molecular_weight	48420.0 kDa
Excluded volume excluded_volume	59655 Å³
Envelope volume envelope_volume	71149 Å³
Hydration-shell volume shell_volume	24320 Å³
Envelope diameter envelope_diameter	86.7 Å
Shell Rg shell_rg	31.56 Å
Envelope Rg envelope_rg	25.27 Å
Shape Rg shape_rg	25.11 Å
Total Rg total_rg	26.02 Å
Total atoms total_atoms	3368
Residues n_residues	438
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	84.8 Å
Rg (real space) rg_real	26.22 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	4.2480e+07
I(0) uncertainty (real space) i0_real_error	6.3950e+05
Rg (reciprocal space) rg_reciprocal	26.20 Å
I(0) (reciprocal space) i0_reciprocal	42480000.0000
Solution quality estimate total_estimate	0.8817
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.612
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10650000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.916; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Kallikrein-4
Molecular weight formula_weight	23926.0 kDa
EC 编号 ec_number	3.4.21.-
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	3658

IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	P-AMINO BENZAMIDINE
Molecular weight formula_weight	136.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	290

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bdga_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.0 — automated matches

Domain ID domain_id	d2bdgb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2bdgA01
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	2bdgA02
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	2bdgB01
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	2bdgB02
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

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8. Citations (1)

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Unit-cell length a length_a	95.680 Å
Unit-cell length b length_b	95.680 Å
Unit-cell length c length_c	38.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.1690
R_work r_work	0.1690
R_free r_free	0.2250

fit	/app/data/saxs_computation/bd/2bdg/2bdg.fit
pddf	/app/data/pr_computation/bd/2bdg/2bdg.pr.out
profile	/app/data/saxs_computation/bd/2bdg/2bdg.dat