6d87

Structure of the Bovine p85alpha BH domain, R262T mutant

Method: X-RAY DIFFRACTION D_max: 79.4 Å Quality: EXCELLENT

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

Phosphatidylinositol 3-kinase regulatory subunit alpha

Bos taurus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 110–302 Chain B； UniProt 110–302	Mutation：R262T Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100 mM Na Cacodylate, pH 6.0	Resolution 2.70 Å R-free 0.238

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 6D87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BFI SOLUTION STRUCTURE OF THE C-TERMINAL SH2 DOMAIN OF THE P85ALPHA REGULATORY SUBUNIT OF PHOSPHOINOSITIDE 3-KINASE, NMR, 30 STRUCTURES Deposited 1997-11-18	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 614–724（111 aa） Fragment：C TERMINAL SH2 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；290 K；Ionic strength (raw mmCIF value) 50 mM；Pressure 1	Resolution not provided
1BFJ SOLUTION STRUCTURE OF THE C-TERMINAL SH2 DOMAIN OF THE P85ALPHA REGULATORY SUBUNIT OF PHOSPHOINOSITIDE 3-KINASE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-11-18	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 614–724（111 aa） Fragment：C TERMINAL SH2 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；290 K；Ionic strength (raw mmCIF value) 50 mM；Pressure 1	Resolution not provided
1OO3 P395S mutant of the p85 regulatory subunit of the N-terminal src homology 2 domain of PI3-Kinase Deposited 2003-03-03	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 321–431（111 aa） Fragment：p85 N-SH2	Mutation：P395S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1M KCl；Pressure ambient NMR sample composition 1.5mM P395S-15N,13C, 0.1M KCl \| 90% H2O/10% D2O	Resolution not provided
1OO4 P395S mutant of the p85 regulatory subunit of the N-terminal src homology 2 domain of PI3-Kinase complexed to a peptide derived from PDGFr Deposited 2003-03-03	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 A 321–431（111 aa） Fragment：p85 N-SH2	Mutation：P395S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1M KCl；Pressure ambient NMR sample composition 1.5mM P395S-15N, 13C, 0.1M KCl \| 90% H2O/10% D2O	Resolution not provided
1PNJ SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE SH3 DOMAIN OF THE P85ALPHA SUBUNIT OF PHOSPHATIDYLINOSITOL 3-KINASE Deposited 1993-07-19	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 1–84（84 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1QAD Crystal Structure of the C-Terminal SH2 Domain of the P85 alpha Regulatory Subunit of Phosphoinositide 3-Kinase: An SH2 domain mimicking its own substrate Deposited 1999-02-26	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 614–724（111 aa） Fragment：C-TERMINAL SH2 DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SPONTANEOUS CRYSTALLISATION；pH 7.5；277 K；TRIS-HCL, NACL, EDTA, DTT, pH 7.5, SPONTANEOUS CRYSTALLISATION, temperature 277.0K	Resolution 1.80 Å R-free 0.236
2PNA STRUCTURE OF AN SH2 DOMAIN OF THE P85 ALPHA SUBUNIT OF PHOSPHATIDYLINOSITOL-3-OH KINASE Deposited 1992-06-30	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 328–431（104 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2PNB STRUCTURE OF AN SH2 DOMAIN OF THE P85 ALPHA SUBUNIT OF PHOSPHATIDYLINOSITOL-3-OH KINASE Deposited 1992-06-30	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 328–431（104 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2PNI SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE SH3 DOMAIN OF THE P85ALPHA SUBUNIT OF PHOSPHATIDYLINOSITOL 3-KINASE Deposited 1993-07-19	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 1–84（84 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5DXH p110alpha/p85alpha with compound 5 Deposited 2015-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 431–599（169 aa） Fragment：UNP residues 431-599	Not recorded	5H2 methyl {2-[4-(2-chlorophenyl)-4H-1,2,4-triazol-3-yl]-4,5-dihydrothieno[3,2-d][1]benzoxepin-8-yl}carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 20000	Resolution 3.00 Å R-free 0.218
5DXH p110alpha/p85alpha with compound 5 Deposited 2015-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 431–599（169 aa） Fragment：UNP residues 431-599	Not recorded	5H2 methyl {2-[4-(2-chlorophenyl)-4H-1,2,4-triazol-3-yl]-4,5-dihydrothieno[3,2-d][1]benzoxepin-8-yl}carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 20000	Resolution 3.00 Å R-free 0.218
5DXU p110delta/p85alpha with GDC-0326 Deposited 2015-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 431–599（169 aa） Fragment：UNP residues 431-599	Not recorded	5H5 (2S)-2-({2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}oxy)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG	Resolution 2.64 Å R-free 0.284
5T8F p110delta/p85alpha with taselisib (GDC-0032) Deposited 2016-09-07	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 B 431–599（169 aa） Fragment：PI3-KINASE P110 DELTA AND P85 FRAGMENT	Not recorded	799 2-methyl-2-(4-{2-[3-methyl-1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}-1H-pyrazol-1-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG	Resolution 2.91 Å R-free 0.304
6D81 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–302（193 aa） Chain B 110–302（193 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, pH 6.0, 100mM Na Cacodylate	Resolution 2.25 Å R-free 0.213
6D81 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–302（193 aa）	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 6；293 K；1.5 M Li2SO4, pH 6.0, 100mM Na Cacodylate	Resolution 2.25 Å R-free 0.213
6D81 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–302（193 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, pH 6.0, 100mM Na Cacodylate	Resolution 2.25 Å R-free 0.213
6D82 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–302（193 aa） Fragment：residues 110-302 Chain B 110–302（193 aa） Fragment：residues 110-302	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100mM Na Cacodylate pH 6.0	Resolution 2.41 Å R-free 0.228
6D82 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–302（193 aa） Fragment：residues 110-302	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100mM Na Cacodylate pH 6.0	Resolution 2.41 Å R-free 0.228
6D82 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–302（193 aa） Fragment：residues 110-302	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 6；293 K；1.5 M Li2SO4, 100mM Na Cacodylate pH 6.0	Resolution 2.41 Å R-free 0.228
6D85 Structure of the Bovine p85a BH domain E217K mutant Deposited 2018-04-25	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–302（193 aa） Fragment：residues 110-302 Chain B 110–302（193 aa） Fragment：residues 110-302	Mutation：E217K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E217K Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100 mM Na Cacodylate, pH 6.0	Resolution 2.20 Å R-free 0.221
6D85 Structure of the Bovine p85a BH domain E217K mutant Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–302（193 aa） Fragment：residues 110-302	Mutation：E217K Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100 mM Na Cacodylate, pH 6.0	Resolution 2.20 Å R-free 0.221
6D85 Structure of the Bovine p85a BH domain E217K mutant Deposited 2018-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–302（193 aa） Fragment：residues 110-302	Mutation：E217K 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 6；293 K；1.5 M Li2SO4, 100 mM Na Cacodylate, pH 6.0	Resolution 2.20 Å R-free 0.221
6D86 Structure of the Bovine p85a BH domain Deposited 2018-04-25	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–302（193 aa） Chain B 110–302（193 aa）	Mutation：E297K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E297K Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5 M Li2SO4, 100 mM Na Cacodylate, pH 6.0	Resolution 2.30 Å R-free 0.214
6G6W HUMAN PI3KDELTA IN COMPLEX WITH LIGAND LASW1976 Deposited 2018-04-03	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 B 431–599（169 aa） Fragment：UNP residues 431-599	Not recorded	EO5 ~{N}-[3-[4-[[(1~{S})-1-(5-methyl-4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]-7~{H}-pyrrolo[ 2,3-d]pyrimidin-5-yl]-5-oxidanyl-phenyl]methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG	Resolution 2.72 Å R-free 0.260
6MRP Structure of the Bovine p85a BH domain R228E mutant Deposited 2018-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–319（210 aa） Chain B 110–319（210 aa）	Mutation：R228E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R228E 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 6.1；298 K；1.5 M Li2SO4, 4% glycerol, 0.1 Sodium Cacodylate buffer	Resolution 2.40 Å R-free 0.225
6MRP Structure of the Bovine p85a BH domain R228E mutant Deposited 2018-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–319（210 aa）	Mutation：R228E 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 6.1；298 K；1.5 M Li2SO4, 4% glycerol, 0.1 Sodium Cacodylate buffer	Resolution 2.40 Å R-free 0.225
6MRP Structure of the Bovine p85a BH domain R228E mutant Deposited 2018-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–319（210 aa）	Mutation：R228E 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 6.1；298 K；1.5 M Li2SO4, 4% glycerol, 0.1 Sodium Cacodylate buffer	Resolution 2.40 Å R-free 0.225
6OCO HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 6 Deposited 2019-03-25	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 B 431–600（170 aa）	Not recorded	M5V 4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl)pyrimidine-5-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；16.60 % PEG6000 0.10 M KCl 0.10 M MES pH=6.00	Resolution 2.58 Å R-free 0.296
6OCU HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 29 Deposited 2019-03-25	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 B 431–600（170 aa）	Not recorded	M5D 5-{(3R)-3-methyl-4-[(1R,2R)-2-methylcyclopropane-1-carbonyl]piperazin-1-yl}-3-(1-methyl-1H-pyrazol-4-yl)pyrazine-2-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；16% PEG6000 0.10 M KCl 0.10 M MES pH 6.0	Resolution 2.77 Å R-free 0.287
6R4R Cryo-EM Structure of the PI3-Kinase SH3 Domain Amyloid Fibril Deposited 2019-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 1–84（84 aa） Chain B 1–84（84 aa） Chain C 1–84（84 aa） Chain D 1–84（84 aa） Chain E 1–84（84 aa） Chain F 1–84（84 aa） Chain G 1–84（84 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 2.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7JIS HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 2F Deposited 2020-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 431–599（169 aa）	Not recorded	VBS (3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；16% PEG6000, 0.10 M KCL, 0.10 M MES pH 6.0	Resolution 2.42 Å R-free 0.267
8BCY HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 13 Deposited 2022-10-17	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 B 431–599（169 aa）	Not recorded	I3H 9-[2-(3,4-dichlorophenyl)ethyl]-2-(3-hydroxyphenyl)-8-oxidanylidene-7~{H}-purine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG6000, 0.10 M KCL, 0.10 M MES	Resolution 2.43 Å R-free 0.263
8S3R HUMAN PI3KDELTA IN COMPLEX WITH PYRIDAZINONE INHIBITOR 7 Deposited 2024-02-20	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 B 431–599（169 aa）	Not recorded	A1H48 5-[(1~{S})-1-[4-azanyl-3-(5-oxidanylpyridin-3-yl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-cyclopentyl-2-(phenylmethyl)pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG6000, 0.10 M KCL, 0.10 M MES	Resolution 2.28 Å R-free 0.270
9GCF HUMAN PI3KDELTA IN COMPLEX WITH ISOCUMARIN INHIBITOR CHF-6523 Deposited 2024-08-01	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 B 431–600（170 aa）	Not recorded	A1IJ5 3-[(1S)-1-[4-azanyl-3-(5-oxidanylpyridin-3-yl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-[3-[(4-methylpiperazin-1-yl)methyl]phenyl]isochromen-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG6000, 0.10 M KCL, 0.10 M MES	Resolution 2.89 Å R-free 0.296
9GDI HUMAN PI3KDELTA IN COMPLEX WITH ISOCUMARIN INHIBITOR 10 Deposited 2024-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 431–600（170 aa）	Not recorded	A1IJ1 3-[(1S)-1-[4-azanyl-3-(3-fluoranyl-5-oxidanyl-phenyl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-(1-methyl-3,6-dihydro-2H-pyridin-4-yl)isochromen-1-one × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG6000, 0.10 M KCL, 0.10 M MES	Resolution 2.81 Å R-free 0.299
9L3R Human PI3KDELTA in complex with Zandelisib Deposited 2024-12-19	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 B 431–600（170 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	A1L62 Zandelisib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；283.15 K；10% PEG 4000, 100 mM KCl, 1 mM TCEP neutral pH, 10 mM CaCl2, 100 mM MES pH 5.8	Resolution 2.50 Å R-free 0.278

27 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P85A_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 110–302 Author chain B； PDBConstruct 1–193； UniProt 110–302

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	6d87
Deposition date deposition_date	2018-04-25
Structure title title	Structure of the Bovine p85alpha BH domain, R262T mutant
Keywords keywords	GAP protein, SIGNALING PROTEIN; SIGNALING PROTEIN
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	25.42 Å
Radius of gyration Rg (electron density) rg_electron	24.28 Å
Forward intensity I(0) i0	24114200.00
Molecular weight molecular_weight	40106.0 kDa
Excluded volume excluded_volume	51402 Å³
Envelope volume envelope_volume	61756 Å³
Hydration-shell volume shell_volume	22095 Å³
Envelope diameter envelope_diameter	80.6 Å
Shell Rg shell_rg	30.18 Å
Envelope Rg envelope_rg	24.23 Å
Shape Rg shape_rg	24.23 Å
Total Rg total_rg	25.23 Å
Total atoms total_atoms	5711
Residues n_residues	354
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	79.4 Å
Rg (real space) rg_real	25.46 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.4110e+07
I(0) uncertainty (real space) i0_real_error	3.1990e+05
Rg (reciprocal space) rg_reciprocal	25.45 Å
I(0) (reciprocal space) i0_reciprocal	24110000.0000
Solution quality estimate total_estimate	0.9033
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.319
Kurtosis Kurtosis kurtosis	-0.623
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3322000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.977

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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	Phosphatidylinositol 3-kinase regulatory subunit alpha
Molecular weight formula_weight	21853.1 kDa
Mutation mutation	R262T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5802

QQASTLPDLAEQFAPPDVAPPLLIKLVEAIEKKGLECSTLYRTQSSSNPAELRQLLDCDTASLDLEMFDVHVLADAFKRYLLDLPNPVIPVAVSSELISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTLQYLLKHFFKLSQTSSKNLLNATVLSELFSPLLFRFPAASSENTEHLIKIIEILISTEWNERQ

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	Bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6d87a_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.1 — BCR-homology GTPase activation domain (BH-domain)

Domain ID domain_id	d6d87b_
Class class	a — All alpha proteins
Fold Fold fold	a.116 — GTPase activation domain, GAP
Superfamily Superfamily superfamily	a.116.1 — GTPase activation domain, GAP
Family Family family	a.116.1.1 — BCR-homology GTPase activation domain (BH-domain)

CATH v4.4 (2 domains)

Domain ID domain_id	6d87A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

Domain ID domain_id	6d87B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	555 — Phosphatidylinositol 3-kinase; Chain A
Homologous superfamily homologous superfamily	10 — Rho GTPase activation protein

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8. Citations (1)

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Unit-cell length a length_a	85.499 Å
Unit-cell length b length_b	91.637 Å
Unit-cell length c length_c	93.574 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	35.795 Å
R factor r_factor	0.1980
R_work r_work	0.1961
R_free r_free	0.2382

fit	/app/data/saxs_computation/d8/6d87/6d87.fit
pddf	/app/data/pr_computation/d8/6d87/6d87.pr.out
profile	/app/data/saxs_computation/d8/6d87/6d87.dat