3gm1

Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides

Method: X-RAY DIFFRACTION D_max: 84.9 Å Quality: GOOD

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

Protein tyrosine kinase 2 beta

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 861–1009	Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009 Mutation：C899A	Paxillin × 2 （P49023）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 861–1009	Fragment：Focal Adhesion Targeting (FAT) Domain, UNP residues 861-1009 Mutation：C899A	Paxillin × 2 （P49023）	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

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 3GM1	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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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
3GM2 Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 Deposited 2009-03-12	Different oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 mutation/modification Different oligomeric state 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 32 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 5–153； UniProt 861–1009 Author chain B； PDBConstruct 5–153； UniProt 861–1009

Paxillin

OrganismNot specified

UniProt P49023

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 262–274 Chain F； UniProt 262–274	Fragment：Paxillin LD4 Motif, UNP residues 262-274	Protein tyrosine kinase 2 beta × 1 （Q14289）	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 262–274 Chain D； UniProt 262–274	Fragment：Paxillin LD4 Motif, UNP residues 262-274	Protein tyrosine kinase 2 beta × 1 （Q14289）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3GM1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2O9V The second SH3 domain from Ponsin in complex with the paxillin proline rich region Deposited 2006-12-14	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 B 45–54（10 aa） Fragment：Proline rich region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.2M Sodium Acetate, 0.1M Sodium Cacodylate, 30% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.63 Å R-free 0.177
2VZD Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif Deposited 2008-07-31	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 C 1–20（20 aa） Fragment：PAXILLIN LD1 MOTIF, RESIDUES 1-20	Not recorded	PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% (W/V) PEG 10000, 0.1M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255
2VZD Crystal structure of the C-terminal calponin homology domain of alpha parvin in complex with paxillin LD1 motif Deposited 2008-07-31	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 1–20（20 aa） Fragment：PAXILLIN LD1 MOTIF, RESIDUES 1-20	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；20% (W/V) PEG 10000, 0.1M HEPES PH 7.5	Resolution 2.10 Å R-free 0.255
2VZG Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD2 motif Deposited 2008-08-01	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 8–27（20 aa） Fragment：PAXILLIN LD1 MOTIF, RESIDUES 141-160	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；286 K；40% (W/V) PEG200, 0.1 M CITRATE PH 4.5	Resolution 1.80 Å R-free 0.221
2VZI Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD4 motif Deposited 2008-08-01	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 262–277（16 aa） Fragment：;PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA,PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA ; Chain A 312–315（4 aa） Fragment：;PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA,PAXILLIN LD4 MOTIF, RESIDUES 262-277 AND 312-315 OF PAXILLIN ISOFORM BETA ;	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；286 K；40%(W/V) PEG 300, 0.1M CITRATE PH 5.2	Resolution 2.20 Å R-free 0.260
3PY7 Crystal structure of full-length Bovine Papillomavirus oncoprotein E6 in complex with LD1 motif of paxillin at 2.3A resolution Deposited 2010-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–10（10 aa）	Mutation：D108A,K109A,K265A,E385A,K388A,D389A (maltose-binding periplasmic protein)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；1.6 M ammonium sulfate, 2% PEG2000 MME 0.1 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.29 Å R-free 0.225
3U3F Structural basis for the interaction of Pyk2 PAT domain with paxillin LD motifs Deposited 2011-10-05	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 261–277（17 aa） Fragment：unp residues 261-277 Chain I 261–277（17 aa） Fragment：unp residues 261-277	Not recorded	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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 261–277（17 aa） Fragment：unp residues 261-277 Chain J 261–277（17 aa） Fragment：unp residues 261-277	Not recorded	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 G 261–277（17 aa） Fragment：unp residues 261-277	Not recorded	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 H 261–277（17 aa） Fragment：unp residues 261-277	Not recorded	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
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	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 K 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	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 L 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	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 M 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	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 N 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
4EDN Crystal structure of beta-parvin CH2 domain in complex with paxillin LD1 motif Deposited 2012-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 1–20（20 aa） Fragment：LD1 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2.1M Ammonium sulfate, 0.01M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.265
6U4M Solution structure of paxillin LIM4 Deposited 2019-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 527–591（65 aa） Fragment：LIM4 domain residues 527-591	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition 1.45 mM [U-13C; U-15N] Paxillin LIM4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6U4N Solution structure of paxillin LIM4 in complex with kindlin-2 F0 Deposited 2019-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 527–591（65 aa） Fragment：LIM4 domain residues 527-591	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient NMR sample composition 0.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 99.8% D2O \| 99.8% D2O NMR sample composition 0.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 99.8% D2O \| 99.8% D2O	Resolution not provided
7QB0 Solution structure of paxillin LIM2/3 Deposited 2021-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 380–499（120 aa）	Not recorded	ZN ZINC ION × 4	SOLUTION NMR NMR measurement conditions pH 7.5；298.15 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure 1 NMR sample composition 500 uM [U-13C; U-15N] Paxillin LIM2/3, 150 mM sodium chloride, 50 mM sodium phosphate, 4 mM sodium azide, 1 mM DTT, 0.1 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 500 uM [U-13C; U-15N] Paxillin LIM2/3, 150 mM sodium chloride, 50 mM sodium phosphate, 4 mM sodium azide, 1 mM DTT, 0.1 mM DSS, 100% D2O \| 100% D2O	Resolution not provided
9QWO Vinculin tail bound to paxillin LD2 Deposited 2025-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 140–158（19 aa） Chain F 140–158（19 aa）	Not recorded	SO4 SULFATE ION × 8 ACT ACETATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；1.26 M (NH4)2SO4, 0.2 M NaCl, 0.1 M Na Acetate pH4.5	Resolution 2.54 Å R-free 0.259

11 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAXI_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 262–274 Author chain D； PDBConstruct 1–13； UniProt 262–274 Author chain E； PDBConstruct 1–13； UniProt 262–274 Author chain F； PDBConstruct 1–13； UniProt 262–274

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	3gm1
Deposition date deposition_date	2009-03-12
Structure title title	Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides
Keywords keywords	four-helix bundle, LD4 motif, TRANSFERASE; 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	23.78 Å
Radius of gyration Rg (electron density) rg_electron	22.95 Å
Forward intensity I(0) i0	22199100.00
Molecular weight molecular_weight	35909.0 kDa
Excluded volume excluded_volume	45152 Å³
Envelope volume envelope_volume	55149 Å³
Hydration-shell volume shell_volume	21020 Å³
Envelope diameter envelope_diameter	89.4 Å
Shell Rg shell_rg	28.77 Å
Envelope Rg envelope_rg	23.15 Å
Shape Rg shape_rg	22.96 Å
Total Rg total_rg	23.67 Å
Total atoms total_atoms	2511
Residues n_residues	328
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	84.9 Å
Rg (real space) rg_real	23.88 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.2200e+07
I(0) uncertainty (real space) i0_real_error	2.9790e+05
Rg (reciprocal space) rg_reciprocal	23.86 Å
I(0) (reciprocal space) i0_reciprocal	22200000.0000
Solution quality estimate total_estimate	0.8414
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.9 Å
Skewness Skewness skewness	0.484
Kurtosis Kurtosis kurtosis	-0.085
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8577000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.810; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein tyrosine kinase 2 beta
Molecular weight formula_weight	16692.2 kDa
EC 编号 ec_number	2.7.10.2
Mutation mutation	C899A
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	2528

GSHMRLGAQSIQPTANLDRTDDLVYLNVMELVRAVLELKNELAQLPPEGYVVVVKNVGLTLRKLIGSVDDLLPSLPSSSRTEIEGTQKLLNKDLAELINKMRLAQQNAVTSLSEECKRQMLTASHTLAVDAKNLLDAVDQAKVLANLAHPPAE

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 polymer

Description description	Paxillin
Molecular weight formula_weight	1436.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,C,D

ATRELDELMASLS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3gm1a_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.14 — FAT domain of focal adhesion kinase
Family Family family	a.24.14.0 — automated matches

Domain ID domain_id	d3gm1b_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.14 — FAT domain of focal adhesion kinase
Family Family family	a.24.14.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3gm1A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

Domain ID domain_id	3gm1B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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8. Citations (1)

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Unit-cell length a length_a	73.774 Å
Unit-cell length b length_b	73.774 Å
Unit-cell length c length_c	156.925 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	42.670 Å
R factor r_factor	0.2359
R_work r_work	0.2331
R_free r_free	0.2899

fit	/app/data/saxs_computation/gm/3gm1/3gm1.fit
pddf	/app/data/pr_computation/gm/3gm1/3gm1.pr.out
profile	/app/data/saxs_computation/gm/3gm1/3gm1.dat

Crystal Structure of the Focal Adhesion Targeting (FAT) Domain of Pyk2 in Complex with Paxillin LD4 Motif-Derived Peptides

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

Paxillin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)