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4h1m

Crystal structure of PYK2 with the indole 10c

Method: X-RAY DIFFRACTION Dmax: 64.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein-tyrosine kinase 2-beta

Homo sapiens

UniProt Q14289

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：protein kinase domain (UNP residues 416-692) 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

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 4H1M 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 ligand/ion 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
3FZO Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase Deposited 2009-01-26 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：UNP residues 416-692, Protein kinase domain
Not recorded No recorded non-water small molecule 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
3FZP Crystal structure of PYK2 complexed with ATPgS Deposited 2009-01-26 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：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 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：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 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：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 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：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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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
4R32 Crystal Structure Analysis of Pyk2 and Paxillin LD motifs Deposited 2014-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 17–293； 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

SAXS profile for 4h1m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4h1m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4h1m
Deposition date deposition_date2012-09-10
Structure title titleCrystal structure of PYK2 with the indole 10c
Keywords keywordskinase, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.06 Å
Radius of gyration Rg (electron density) rg_electron19.27 Å
Forward intensity I(0) i028114000.00
Molecular weight molecular_weight27870.0 kDa
Excluded volume excluded_volume27299 ų
Envelope volume envelope_volume44332 ų
Hydration-shell volume shell_volume19358 ų
Envelope diameter envelope_diameter65.4 Å
Shell Rg shell_rg25.41 Å
Envelope Rg envelope_rg19.57 Å
Shape Rg shape_rg19.26 Å
Total Rg total_rg19.95 Å
Total atoms total_atoms2108
Residues n_residues256
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax64.7 Å
Rg (real space) rg_real20.02 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real2.8110e+07
I(0) uncertainty (real space) i0_real_error3.1640e+05
Rg (reciprocal space) rg_reciprocal20.03 Å
I(0) (reciprocal space) i0_reciprocal28110000.0000
Solution quality estimate total_estimate0.7618
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.280
Kurtosis Kurtosis kurtosis-0.428
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha7322000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 0.406; Positv: 1.000; Valcen: 1.000; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4h1ma_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id4h1mA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4h1mA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)