3fzo

Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase

Method: X-RAY DIFFRACTION D_max: 64.3 Å Quality: EXCELLENT

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

Protein tyrosine kinase 2 beta

OrganismNot specified

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 416–692	Fragment：UNP residues 416-692, Protein kinase domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Bis-Tris, 0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.265

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 3FZO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LK4 Structural and mechanistic insights into the interaction between PAT Pyk2 and Paxillin LD motif Deposited 2011-10-04	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 871–1005（135 aa） Fragment：Focal adhesion targeting (FAT) region residues 871-1005	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.2；305 K；Ionic strength (raw mmCIF value) 7；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] MES, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CC6 Crystal structure of kinase domain of protein tyrosine kinase 2 beta (PTK2B) Deposited 2008-02-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 414–692（279 aa） Fragment：Kinase domain: Residues 414-692	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.05M Magnesium chloride, 0.1M Bis-tris, 17.5% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.219
3ET7 Crystal structure of PYK2 complexed with PF-2318841 Deposited 2008-10-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa）	Not recorded	349 5-{[4-{[2-(pyrrolidin-1-ylsulfonyl)benzyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,3-dihydro-2H-indol-2-one × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；VAPOR DIFFUSION	Resolution 2.70 Å R-free 0.328
3FZP Crystal structure of PYK2 complexed with ATPgS Deposited 2009-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：UNP residues 416-692, Protein kinase domain	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1M Citrate, 0.5-1.5M Lithium Sulfate, 0.2-0.4M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.239
3FZR Crystal structure of PYK2 complexed with PF-431396 Deposited 2009-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：UNP residues 416-692, Protein kinase domain	Not recorded	3JZ N-methyl-N-{2-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]phenyl}methanesulfonamide × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；0.1M Bis-Tris, 0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.70 Å R-free 0.274
3FZS Crystal Structure of PYK2 complexed with BIRB796 Deposited 2009-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：UNP residues 416-692, Protein kinase domain	Not recorded	B96 1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M Bis-Tris, 0.2M MgCls, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.75 Å R-free 0.224
3FZT Crystal structure of PYK2 complexed with PF-4618433 Deposited 2009-01-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：UNP residues 416-692, Protein kinase domain	Not recorded	4JZ 1-[5-tert-butyl-2-(4-methylphenyl)-1,2-dihydro-3H-pyrazol-3-ylidene]-3-{3-[(pyridin-3-yloxy)methyl]-1H-pyrazol-5-yl}urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M Bis-Tris, 0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.95 Å R-free 0.242
3GM1 Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides Deposited 2009-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 861–1009（149 aa） Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009	Mutation：C899A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；4.1 M NaCl, 100 mM HEPES, 5% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.290
3GM1 Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides Deposited 2009-03-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 861–1009（149 aa） Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009	Mutation：C899A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；4.1 M NaCl, 100 mM HEPES, 5% glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.95 Å R-free 0.290
3GM2 Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 Deposited 2009-03-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 861–1009（149 aa） Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009	Mutation：C899A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；298 K；3.4 M NaCl, 100 mM HEPES, 1% glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.71 Å R-free 0.295
3GM3 Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 Deposited 2009-03-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 861–1009（149 aa） Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009	Mutation：C899A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.289
3H3C Crystal structure of PYK2 in complex with Sulfoximine-substituted trifluoromethylpyrimidine analog Deposited 2009-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa）	Not recorded	SO4 SULFATE ION × 5 P1E 4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-N-methylbenzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, 0.1M bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.273
3U3F Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs Deposited 2011-10-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 871–1005（135 aa） Fragment：unp residues 871-1005	Mutation：C899S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；291.2 K；The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K	Resolution 3.10 Å R-free 0.266
3U3F Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs Deposited 2011-10-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 871–1005（135 aa） Fragment：unp residues 871-1005	Mutation：C899S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；291.2 K；The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K	Resolution 3.10 Å R-free 0.266
3U3F Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs Deposited 2011-10-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 871–1005（135 aa） Fragment：unp residues 871-1005	Mutation：C899S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；291.2 K；The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K	Resolution 3.10 Å R-free 0.266
3U3F Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs Deposited 2011-10-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 871–1005（135 aa） Fragment：unp residues 871-1005	Mutation：C899S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.3；291.2 K；The 4 ul drop contained 2 ul protein-LD4 peptide mixture (20mM Mes, pH6.2, 1mM protein, 2 mM peptide) and 2 ul ML (100 mM MES pH6.3, 4.2 M NaCl, 2%(v/v) glycerol., VAPOR DIFFUSION, SITTING DROP, temperature 291.2K	Resolution 3.10 Å R-free 0.266
4EKU Crystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2 Deposited 2012-04-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–409（389 aa） Fragment：UNP residues 21-409	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；1 M AMMONIUM CITRATE TRIBASIC, pH 7.0, 0.1 M BIS-TRIS PROPANE pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.25 Å R-free 0.212
4EKU Crystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2 Deposited 2012-04-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–409（389 aa） Fragment：UNP residues 21-409	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；1 M AMMONIUM CITRATE TRIBASIC, pH 7.0, 0.1 M BIS-TRIS PROPANE pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.25 Å R-free 0.212
4H1J Crystal structure of PYK2 with the pyrazole 13a Deposited 2012-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：protein kinase domain (UNP residues 416-692)	Not recorded	0YH 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(4-methoxy-2-methylphenyl)-1H-pyrazol-5-yl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M Bis-Tris, 0.2 M magnesium chloride, 20-27% PEG3350, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.209
4H1M Crystal structure of PYK2 with the indole 10c Deposited 2012-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa） Fragment：protein kinase domain (UNP residues 416-692)	Not recorded	0YJ 7-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)-N-(propan-2-yl)-1H-indole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；295 K；0.1 M Bis-Tris, 0.2 M magnesium chloride, 20-27% PEG3350, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, temperature 295K	Resolution 1.99 Å R-free 0.296
4R32 Crystal Structure Analysis of Pyk2 and Paxillin LD motifs Deposited 2014-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 871–1005（135 aa） Fragment：Focal Adhesion Targeting (FAT) domain (UNP residues 871-1005)	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；THE WELL SOLUTION CONTAINED 100 mM TRIS, 2.0 M AMMONIUM PHOSPHATE MONOBASIC. THE 4 UL DROP CONTAINED 2 uL OF WELL SOLUTION PLUS 2 uL MIXTURE OF PYK2 AND LD2 IN 20 MM MES, PH 6.0, AT 1 mM PROTEIN TO 2 mM PEPTIDE RATIO , VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.50 Å R-free 0.240
4XEF Pyk2-FAT complexed with Leupaxin LD motif LD1 Deposited 2014-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 871–1005（135 aa） Fragment：FAT domain (UNP residues 871-1005)	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；400 nl drop contained 200 nl protein/LD1 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 200 nl well solution (100 mM Tris, pH 8.5, 0.2 M MgCl2, and 30% PEG 4000).	Resolution 2.50 Å R-free 0.266
4XEF Pyk2-FAT complexed with Leupaxin LD motif LD1 Deposited 2014-12-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 871–1005（135 aa） Fragment：FAT domain (UNP residues 871-1005)	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；400 nl drop contained 200 nl protein/LD1 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 200 nl well solution (100 mM Tris, pH 8.5, 0.2 M MgCl2, and 30% PEG 4000).	Resolution 2.50 Å R-free 0.266
4XEK Pyk2-FAT domain in complex with leupaxin LD4 motif Deposited 2014-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 871–1005（135 aa） Fragment：FAT domain (UNP residues 871-1005)	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291.2 K；4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES, pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM Tris pH 9.0 and 45 % PEG 600)	Resolution 1.79 Å R-free 0.231
4XEV Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide Deposited 2014-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 871–1005（135 aa）	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.2 K；The 4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM MES pH 6.5 and 25 % PEG 3000).	Resolution 2.01 Å R-free 0.250
4XEV Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide Deposited 2014-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 871–1005（135 aa）	Mutation：C899S, C972A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291.2 K；The 4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM MES pH 6.5 and 25 % PEG 3000).	Resolution 2.01 Å R-free 0.250
5TO8 Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency Deposited 2016-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 414–692（279 aa） Fragment：UNP Residues 414-692	Not recorded	7FM 25-(methylsulfonyl)-8-(trifluoromethyl)-5,17,18,21,22,23,24,25-octahydro-12H-7,11-(azeno)-16,13-(metheno)pyrido[3,2-i]pyrrolo[1,2-q][1,3,7,11,17]pentaazacyclohenicosin-20(6H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；19% PEG1000, 100 mM LiSulfate, 50 mM Disodium hydrogen phosphate, 50 mM Citric Acid	Resolution 1.98 Å R-free 0.235
5TOB Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency Deposited 2016-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 414–692（279 aa） Fragment：UNP Residues 414-692	Not recorded	YAM N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；25% PEG3350, 100 mM Bis-Tris pH 5.5, 100 mM MgCl2	Resolution 2.12 Å R-free 0.262
6LF3 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta Deposited 2019-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 790–839（50 aa） Chain B 790–839（50 aa）	Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；30% (v/v) PEG 400, 0.1M CAPS/Sodium hydroxide	Resolution 3.20 Å R-free 0.284
6LF3 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta Deposited 2019-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 790–839（50 aa） Chain D 790–839（50 aa）	Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；30% (v/v) PEG 400, 0.1M CAPS/Sodium hydroxide	Resolution 3.20 Å R-free 0.284
6LF3 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the protein-tyrosine kinase 2-beta Deposited 2019-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 790–839（50 aa） Chain F 790–839（50 aa）	Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A Mutation：surface entropy reduction mutant, D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；30% (v/v) PEG 400, 0.1M CAPS/Sodium hydroxide	Resolution 3.20 Å R-free 0.284
8XOX The Crystal Structure of FAK2 from Biortus. Deposited 2024-01-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa）	Not recorded	YAM N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M LiCl2, 0.1M Tris pH8.0, 20% PEG 6000	Resolution 1.90 Å R-free 0.230
8YGX Structure of the PYK2 from Biortus. Deposited 2024-02-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 416–692（277 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M MgCl2, 0.1M Bis-Tris pH5.5-5.9, 19-29% PEG3,350,1mM TCEP	Resolution 2.00 Å R-free 0.270

24 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FAK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–277； UniProt 416–692

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	3fzo
Deposition date deposition_date	2009-01-26
Structure title title	Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase
Keywords keywords	;tyrosine kinase, dfg-out, Alternative splicing, ATP-binding, Cell membrane, Cytoplasm, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, Polymorphism, Transferase, Tyrosine-protein kinase ;; TRANSFERASE
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	20.43 Å
Radius of gyration Rg (electron density) rg_electron	19.45 Å
Forward intensity I(0) i0	15078700.00
Molecular weight molecular_weight	30340.0 kDa
Excluded volume excluded_volume	38446 Å³
Envelope volume envelope_volume	45034 Å³
Hydration-shell volume shell_volume	19540 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	25.50 Å
Envelope Rg envelope_rg	19.69 Å
Shape Rg shape_rg	19.45 Å
Total Rg total_rg	20.35 Å
Total atoms total_atoms	2129
Residues n_residues	262
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	64.3 Å
Rg (real space) rg_real	20.37 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.5080e+07
I(0) uncertainty (real space) i0_real_error	2.1130e+05
Rg (reciprocal space) rg_reciprocal	20.39 Å
I(0) (reciprocal space) i0_reciprocal	15080000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3784000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3fzoa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id	3fzoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3fzoA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	37.284 Å
Unit-cell length b length_b	96.976 Å
Unit-cell length c length_c	43.066 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2067
R_work r_work	0.2037
R_free r_free	0.2654

Description description	Protein tyrosine kinase 2 beta
Molecular weight formula_weight	32190.3 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2257

Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase

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

Protein tyrosine kinase 2 beta

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

fit	/app/data/saxs_computation/fz/3fzo/3fzo.fit
pddf	/app/data/pr_computation/fz/3fzo/3fzo.pr.out
profile	/app/data/saxs_computation/fz/3fzo/3fzo.dat