4hzs

Crystal structure of Ack1 kinase domain with C-terminal SH3 domain

Method: X-RAY DIFFRACTION D_max: 196.9 Å Quality: REASONABLE

▼

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

Activated CDC42 kinase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 115–453	Fragment：protein kinase and SH3 domains (UNP residues 115-453)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 3.23 Å R-free 0.270
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 115–453	Fragment：protein kinase and SH3 domains (UNP residues 115-453)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 3.23 Å R-free 0.270
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 115–453	Fragment：protein kinase and SH3 domains (UNP residues 115-453)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 3.23 Å R-free 0.270
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 115–453	Fragment：protein kinase and SH3 domains (UNP residues 115-453)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；286 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 3.23 Å R-free 0.270

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 4HZS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CF4 CDC42/ACK GTPASE-BINDING DOMAIN COMPLEX Deposited 1999-03-23	Different construct 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 446–489（44 aa） Fragment：GTPASE-BINDING DOMAIN	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	SOLUTION NMR NMR measurement conditions pH 5.5；298 K NMR sample composition [50%2H; 100%15N,13C]-labelled Cdc42, unlabelled f-ACK, 90% H2O/10% \| 90% H2O/10% D2O NMR sample composition [U-15N] f-ACK, Cdc42, 90% H2O/10% \| 90% H2O/10% D2O NMR sample composition [U-13C; U-15N] f-ACK, Cdc42, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition [U-13C; U-15N] Cdc42, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition [U-100% 15N] Cdc42, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
1U46 Crystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1 Deposited 2004-07-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 109–395（287 aa） Fragment：Kinase Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 4000, magnesium chloride, sodium chloride, HEPES, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.00 Å R-free 0.249
1U46 Crystal Structure of the Unphosphorylated Kinase Domain of the Tyrosine Kinase ACK1 Deposited 2004-07-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 109–395（287 aa） Fragment：Kinase Domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 4000, magnesium chloride, sodium chloride, HEPES, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.00 Å R-free 0.249
1U4D Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine Deposited 2004-07-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–296（287 aa） Fragment：Kinase Domain	Not recorded	DBQ DEBROMOHYMENIALDISINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50	Resolution 2.10 Å R-free 0.248
1U4D Structure of the ACK1 Kinase Domain bound to Debromohymenialdisine Deposited 2004-07-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 10–296（287 aa） Fragment：Kinase Domain	Not recorded	DBQ DEBROMOHYMENIALDISINE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291 K；PEG 2000, sodium chloride, magnesium chloride, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 7.50	Resolution 2.10 Å R-free 0.248
1U54 Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP Deposited 2004-07-26	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 109–395（287 aa） Fragment：Kinase Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50	Resolution 2.80 Å R-free 0.322
1U54 Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP Deposited 2004-07-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 109–395（287 aa） Fragment：Kinase Domain	Not recorded	MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50	Resolution 2.80 Å R-free 0.322
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–392（276 aa） Fragment：UNP residues 117-392 Chain B 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.284
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.284
3EQP Crystal Structure of Ack1 with compound T95 Deposited 2008-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T95 N-(2,6-dimethylphenyl)-4-(2-ethoxyphenoxy)-2-({4-[4-(2-hydroxyethyl)piperazin-1-yl]phenyl}amino)pyrimidine-5-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.284
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–392（276 aa） Fragment：UNP residues 117-392 Chain B 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.256
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.256
3EQR Crystal Structure of Ack1 with compound T74 Deposited 2008-10-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 117–392（276 aa） Fragment：UNP residues 117-392	Not recorded	T74 N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.00 Å R-free 0.256
4EWH Co-crystal structure of ACK1 with inhibitor Deposited 2012-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–391（275 aa） Chain B 117–391（275 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	T77 6-{4-[2-(dimethylamino)ethoxy]phenyl}-N-(1,3-dithiolan-2-ylmethyl)-5-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；vapor diffusion, temperature 298K	Resolution 2.50 Å R-free 0.313
4HZR Crystal structure of Ack1 kinase domain Deposited 2012-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 115–389（275 aa） Fragment：protein kinase domain (UNP residues 115-389)	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；286 K；0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 1.31 Å R-free 0.209
4HZR Crystal structure of Ack1 kinase domain Deposited 2012-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 115–389（275 aa） Fragment：protein kinase domain (UNP residues 115-389)	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；286 K；0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K	Resolution 1.31 Å R-free 0.209
4ID7 ACK1 kinase in complex with the inhibitor cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol Deposited 2012-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–389（273 aa） Fragment：Kinase domain, UNP residues 117-389	Not recorded	1G0 cis-3-[8-amino-1-(4-phenoxyphenyl)imidazo[1,5-a]pyrazin-3-yl]cyclobutanol × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions ligang replacement；ligang replacement	Resolution 3.00 Å R-free 0.259
5ZXB Crystal structure of ACK1 with compound 10d Deposited 2018-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 117–391（275 aa） Chain B 117–391（275 aa）	Not recorded	9KO N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.3；291 K；0.1M Bis-Tris pH6.3 0.2M AmSO4 28% PEG3350 10mM DTT	Resolution 2.20 Å R-free 0.257
6VQM Crystal Structure Analysis of human ACK1 Deposited 2020-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 109–395（287 aa） Chain B 109–395（287 aa）	Not recorded	R7P 2-({4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]-2-methoxyphenyl}amino)-9-methyl-5,7-dihydro-6H-pyrimido[5,4-d][1,3]benzodiazepin-6-one × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；PEG4000	Resolution 2.87 Å R-free 0.330
7KP6 Structure of Ack1 kinase in complex with a selective inhibitor Deposited 2020-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–391（282 aa） Fragment：kinase domain	Not recorded	WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；50mM Bis-Tris (pH 6.5), 23 % (w/v) polyethylene glycol 3350, 100 mM MgCl2, and 2.5% Glycerol	Resolution 1.79 Å R-free 0.203
7KP6 Structure of Ack1 kinase in complex with a selective inhibitor Deposited 2020-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–391（282 aa） Fragment：kinase domain	Not recorded	WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；298 K；50mM Bis-Tris (pH 6.5), 23 % (w/v) polyethylene glycol 3350, 100 mM MgCl2, and 2.5% Glycerol	Resolution 1.79 Å R-free 0.203
8FE9 Crystal structure of Ack1 kinase K161Q mutant in complex with the selective inhibitor (R)-9b Deposited 2022-12-06	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 110–391（282 aa）	Mutation：K161Q	WTP 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.05 M Bis-Tris (pH 5.8), 19% PEG3350, 0.3 M MgCl2, 2.5% glycerol	Resolution 3.20 Å R-free 0.228
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27	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 958–1038（81 aa）	Mutation：R45S, V77E	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2	Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 958–1038（81 aa）	Mutation：R45S, V77E	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2	Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 958–1038（81 aa）	Mutation：R45S, V77E	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2	Resolution 2.78 Å R-free 0.267
8FZ3 Sterile Alpha Motif of Human Translocation ETS Leukemia, Non-Polymer Crystal Form Deposited 2023-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 958–1038（81 aa）	Mutation：R45S, V77E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；298 K；1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 8.2	Resolution 2.78 Å R-free 0.267
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 117–389（273 aa）	Not recorded	LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4	Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 117–389（273 aa）	Not recorded	LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4	Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 117–389（273 aa）	Not recorded	LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4	Resolution 3.17 Å R-free 0.264
8HMT The complex of ACK1 with the inhibitor 2-142 Deposited 2022-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 117–389（273 aa）	Not recorded	LWX 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 4000, 0.2M Bis-Tris ph 6.4	Resolution 3.17 Å R-free 0.264
8Q5P Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1 Deposited 2023-08-09	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 B 508–519（12 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M TRIS pH 8.5, 16%w/v PEG 10000	Resolution 1.81 Å R-free 0.246
8THA 1TEL, non-compressed, double-helical crystal form Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 954–1038（85 aa）	Mutation：V112E,R80S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.5 M Bis-Tris, 0.35 M Mg-Formate, 5 mg/mL protein	Resolution 1.68 Å R-free 0.215

17 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–341； UniProt 115–453 Author chain B； PDBConstruct 3–341； UniProt 115–453 Author chain C； PDBConstruct 3–341； UniProt 115–453 Author chain D； PDBConstruct 3–341； UniProt 115–453

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hzs
Deposition date deposition_date	2012-11-15
Structure title title	Crystal structure of Ack1 kinase domain with C-terminal SH3 domain
Keywords keywords	inactive state, allostery, dimerization, oligomerization, negative regulation, activation, phosphotransfer, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	57.42 Å
Radius of gyration Rg (electron density) rg_electron	58.87 Å
Forward intensity I(0) i0	301868000.00
Molecular weight molecular_weight	144990.0 kDa
Excluded volume excluded_volume	181930 Å³
Envelope volume envelope_volume	276030 Å³
Hydration-shell volume shell_volume	44028 Å³
Envelope diameter envelope_diameter	213.1 Å
Shell Rg shell_rg	51.26 Å
Envelope Rg envelope_rg	58.01 Å
Shape Rg shape_rg	58.82 Å
Total Rg total_rg	58.78 Å
Total atoms total_atoms	10196
Residues n_residues	1276
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

▼

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

Maximum dimension Dmax dmax	196.9 Å
Rg (real space) rg_real	58.39 Å
Rg uncertainty (real space) rg_real_error	2.24 Å
I(0) (real space) i0_real	3.0190e+08
I(0) uncertainty (real space) i0_real_error	6.0260e+06
Rg (reciprocal space) rg_reciprocal	56.57 Å
I(0) (reciprocal space) i0_reciprocal	301000000.0000
Solution quality estimate total_estimate	0.7162
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	36.5 Å
Skewness Skewness skewness	0.569
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	7952000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.608; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.353; Smooth: 0.128

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4hzsA01
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	4hzsA02
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

Domain ID domain_id	4hzsB01
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	4hzsB02
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

Domain ID domain_id	4hzsC01
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	4hzsC02
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

Domain ID domain_id	4hzsD01
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	4hzsD02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	145.463 Å
Unit-cell length b length_b	145.463 Å
Unit-cell length c length_c	103.745 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	16

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

Resolution resolution	3.230 Å
Low-resolution limit resolution_low	73.040 Å
R factor r_factor	0.2470
R_work r_work	0.2460
R_free r_free	0.2700

Description description	Activated CDC42 kinase 1
Molecular weight formula_weight	38861.5 kDa
EC 编号 ec_number	2.7.10.2, 2.7.11.1
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10196

Crystal structure of Ack1 kinase domain with C-terminal SH3 domain

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

Activated CDC42 kinase 1

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Spodoptera frugiperda

fit	/app/data/saxs_computation/hz/4hzs/4hzs.fit
pddf	/app/data/pr_computation/hz/4hzs/4hzs.pr.out
profile	/app/data/saxs_computation/hz/4hzs/4hzs.dat