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3x03

Crystal structure of PIP4KIIBETA complex with AMPPNP

Method: X-RAY DIFFRACTION Dmax: 106.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

Homo sapiens

UniProt P78356

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 31–416 Chain B； UniProt 31–416 Fragment：UNP RESIDUES 31-416 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.70 Å R-free 0.280

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 3X03 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BO1 PHOSPHATIDYLINOSITOL PHOSPHATE KINASE TYPE II BETA Deposited 1998-08-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Chain B 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；100MM SODIUM CITRATE PH5.6 200MM MAGNESIUM ACETATE 100MM LITHIUM ACETATE 16% PEG (4000)
Resolution 3.00 Å R-free 0.299
3WZZ Crystal structure of PIP4KIIBETA Deposited 2014-10-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE CONTAININ, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.260
3X01 Crystal structure of PIP4KIIBETA complex with AMP Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Not recorded AMP ADENOSINE MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE CONTAINING 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.15 Å R-free 0.279
3X02 Crystal structure of PIP4KIIBETA complex with GMP Deposited 2014-10-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Not recorded 5GP GUANOSINE-5'-MONOPHOSPHATE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE CONTAINING 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.45 Å R-free 0.255
3X04 Crystal structure of PIP4KIIBETA complex with GMPPNP Deposited 2014-10-09 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.277
3X05 Crystal structure of PIP4KIIBETA T201M complex with AMP Deposited 2014-10-09 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 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：T201M Mutation：T201M AMP ADENOSINE MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.273
3X06 Crystal structure of PIP4KIIBETA T201M complex with GMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：T201M Mutation：T201M 5GP GUANOSINE-5'-MONOPHOSPHATE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.65 Å R-free 0.261
3X07 Crystal structure of PIP4KIIBETA N203A complex with AMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：N203A Mutation：N203A AMP ADENOSINE MONOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.270
3X08 Crystal structure of PIP4KIIBETA N203A complex with GMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：N203A Mutation：N203A 5GP GUANOSINE-5'-MONOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.75 Å R-free 0.267
3X09 Crystal structure of PIP4KIIBETA F205L complex with AMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：F205L Mutation：F205L AMP ADENOSINE MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.70 Å R-free 0.260
3X0A Crystal structure of PIP4KIIBETA F205L complex with GMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：F205L Mutation：F205L 5GP GUANOSINE-5'-MONOPHOSPHATE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.272
3X0B Crystal structure of PIP4KIIBETA I368A complex with AMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：I368A Mutation：I368A AMP ADENOSINE MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.282
3X0C Crystal structure of PIP4KIIBETA I368A complex with GMP Deposited 2014-10-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416
Mutation：I368A Mutation：I368A 5GP GUANOSINE-5'-MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；100MM NA-CITRATE, 10MM MG-ACETATE, 100MM LI-ACETATE, 8-14%(V/V) PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.55 Å R-free 0.268
6K4G Crystal structure of the PI5P4Kbeta-GMPPNP complex Deposited 2019-05-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；293 K；9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate
Resolution 2.70 Å R-free 0.275
6K4H Crystal structure of the PI5P4Kbeta-AMPPNP complex Deposited 2019-05-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate
Resolution 2.55 Å R-free 0.282
7EM1 Crystal structure of the PI5P4Kbeta-ITP complex Deposited 2021-04-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded IDP INOSINE-5'-DIPHOSPHATE × 2 CZU [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate
Resolution 2.65 Å R-free 0.266
7EM2 Crystal structure of the PI5P4Kbeta-XTP complex Deposited 2021-04-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded CZC [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 2 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate
Resolution 2.60 Å R-free 0.258
7EM3 Crystal structure of the PI5P4Kbeta-2a-ATP complex Deposited 2021-04-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded CX0 [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 CXC [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate
Resolution 3.10 Å R-free 0.256
7EM4 Crystal structure of the PI5P4Kbeta F205L-ITP complex Deposited 2021-04-13 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 31–416（386 aa）
Chain B 31–416（386 aa）
Mutation：F205L Mutation：F205L IDP INOSINE-5'-DIPHOSPHATE × 2 CZU [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate
Resolution 2.80 Å R-free 0.278
7EM5 Crystal structure of the PI5P4Kbeta F205L-XTP complex Deposited 2021-04-13 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 31–416（386 aa）
Chain B 31–416（386 aa）
Mutation：F205L Mutation：F205L CZC [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 2 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate
Resolution 2.80 Å R-free 0.261
7EM6 Crystal structure of the PI5P4Kbeta N203D-ITP complex Deposited 2021-04-13 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 31–416（386 aa）
Chain B 31–416（386 aa）
Mutation：N203D Mutation：N203D IDP INOSINE-5'-DIPHOSPHATE × 2 CZU [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate
Resolution 2.95 Å R-free 0.268
7EM7 Crystal structure of the PI5P4Kbeta N203D-XTP complex Deposited 2021-04-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–416（386 aa）
Chain B 31–416（386 aa）
Not recorded CZC [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 CZF [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；9%(W/V) PEG4000, 0.1 M Sodium Citrate pH 6.0, 0.1 M Magnesium Acetate, 0.1 M Lithium Acetate
Resolution 3.45 Å R-free 0.296
7EM8 Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex Deposited 2021-04-13 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 31–416（386 aa）
Chain B 31–416（386 aa）
Mutation：T201M Mutation：T201M CX0 [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate × 1 CXC [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate
Resolution 3.05 Å R-free 0.275
7N80 Crystal Structure of PI5P4KIIBeta Deposited 2021-06-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–416（385 aa）
Chain B 32–416（385 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.15 M DL-Malic acid pH 7.0, 20% (w/v) Polyethylene glycol 3350
Resolution 2.50 Å R-free 0.283
7N81 Crystal Structure of PI5P4KIIBeta complex with CC260 Deposited 2021-06-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–416（385 aa）
Chain B 32–416（385 aa）
Not recorded HKP (7R)-8-cyclopentyl-7-(cyclopentylmethyl)-2-[(3,5-dichloro-4-hydroxyphenyl)amino]-5-methyl-7,8-dihydropteridin-6(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M Sodium bromide, 0.02 M Cadmium chloride, 20% (w/v) Polyethylene glycol 3350
Resolution 2.70 Å R-free 0.281

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PI42B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–393； UniProt 31–416 Author chain B； PDBConstruct 8–393； UniProt 31–416

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3x03

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3x03
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3x03
Deposition date deposition_date2014-10-09
Structure title titleCrystal structure of PIP4KIIBETA complex with AMPPNP
Keywords keywordsLIPID KINASE, PHOSPHOINOSITIDE SIGNALING, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.32 Å
Radius of gyration Rg (electron density) rg_electron33.20 Å
Forward intensity I(0) i088786100.00
Molecular weight molecular_weight74209.0 kDa
Excluded volume excluded_volume92540 ų
Envelope volume envelope_volume123010 ų
Hydration-shell volume shell_volume32883 ų
Envelope diameter envelope_diameter111.5 Å
Shell Rg shell_rg37.43 Å
Envelope Rg envelope_rg33.46 Å
Shape Rg shape_rg33.20 Å
Total Rg total_rg33.57 Å
Total atoms total_atoms5212
Residues n_residues622
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.2 Å
Rg (real space) rg_real33.77 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real8.8790e+07
I(0) uncertainty (real space) i0_real_error1.5320e+06
Rg (reciprocal space) rg_reciprocal33.59 Å
I(0) (reciprocal space) i0_reciprocal88770000.0000
Solution quality estimate total_estimate0.7823
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.543
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56060000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.758; Smooth: 0.124
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3x03a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.143 — SAICAR synthase-like
Superfamily Superfamily superfamilyd.143.1 — SAICAR synthase-like
Family Family familyd.143.1.2 — Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta

CATH v4.4 (4 domains)

Domain ID domain_id3x03A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology800 — Phosphatidylinositol Phosphate Kinase II Beta
Homologous superfamily homologous superfamily10 — Phosphatidylinositol Phosphate Kinase II Beta
Domain ID domain_id3x03A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology810 — Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2
Homologous superfamily homologous superfamily10 — 2-Layer Sandwich
Domain ID domain_id3x03B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology800 — Phosphatidylinositol Phosphate Kinase II Beta
Homologous superfamily homologous superfamily10 — Phosphatidylinositol Phosphate Kinase II Beta
Domain ID domain_id3x03B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology810 — Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2
Homologous superfamily homologous superfamily10 — 2-Layer Sandwich
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8. Citations (1)

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9. Files and Curves (10)