SAXSdb — 7em6

▼

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

Phosphatidylinositol 5-phosphate 4-kinase type-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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–416 Chain B； UniProt 31–416	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

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 7EM6	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 mutation/modification 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 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） 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 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） 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 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） 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
3X03 Crystal structure of PIP4KIIBETA complex with AMPPNP Deposited 2014-10-09	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） Fragment：UNP RESIDUES 31-416 Chain B 31–416（386 aa） Fragment：UNP RESIDUES 31-416	Not recorded	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
3X04 Crystal structure of PIP4KIIBETA complex with GMPPNP Deposited 2014-10-09	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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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） 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 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）	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 mutation/modification 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 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）	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 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）	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 mutation/modification 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 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
7EM7 Crystal structure of the PI5P4Kbeta N203D-XTP complex Deposited 2021-04-13	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）	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 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） 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 mutation/modification 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 mutation/modification 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7em6
Deposition date deposition_date	2021-04-13
Structure title title	Crystal structure of the PI5P4Kbeta N203D-ITP complex
Keywords keywords	Lipid Kinase, Phosphoinositide signaling, 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	32.31 Å
Radius of gyration Rg (electron density) rg_electron	32.08 Å
Forward intensity I(0) i0	73498700.00
Molecular weight molecular_weight	66940.0 kDa
Excluded volume excluded_volume	83100 Å³
Envelope volume envelope_volume	110680 Å³
Hydration-shell volume shell_volume	30662 Å³
Envelope diameter envelope_diameter	109.8 Å
Shell Rg shell_rg	36.36 Å
Envelope Rg envelope_rg	32.71 Å
Shape Rg shape_rg	32.14 Å
Total Rg total_rg	32.25 Å
Total atoms total_atoms	4718
Residues n_residues	612
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	113.6 Å
Rg (real space) rg_real	32.78 Å
Rg uncertainty (real space) rg_real_error	1.05 Å
I(0) (real space) i0_real	7.3500e+07
I(0) uncertainty (real space) i0_real_error	1.4190e+06
Rg (reciprocal space) rg_reciprocal	32.59 Å
I(0) (reciprocal space) i0_reciprocal	73490000.0000
Solution quality estimate total_estimate	0.7110
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.587
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44250000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.555; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.576; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Molecular weight formula_weight	44929.9 kDa
EC 编号 ec_number	2.7.1.149
Mutation mutation	N203D
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	4718

GPNCAPGQKVKLFRASEPILSVLMWGVNHTINELSNVPVPVMLMPDDFKAYSKIKVDNHLFNKENLPSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINSDSQGRCGTRFLTTYDRRFVIKTVSSEDVAEMHNILKKYHQFIVECHGNTLLPQFLGMYRLTVDGVETYMVVTRDVFSHRLTVHRKYDLKGSTVAREASDKEKAKDLPTFKDNDFLNEGQKLHVGEESKKNFLEKLKRDVEFLAQLKIMDYSLLVGIHDVDRAEQEEMEVEERAEDEECENDGVGGNLLCSYGTPPDSPGNLLSFPRFFGPGEFDPSVDVYAMKSHESSPKKEVYFMAIIDILTPYDTKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFNEFMSNILT

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 non-polymer

Description description	INOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	428.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;[[(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 ;
Molecular weight formula_weight	508.2 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7em6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	800 — Phosphatidylinositol Phosphate Kinase II Beta
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol Phosphate Kinase II Beta

Domain ID domain_id	7em6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	800 — Phosphatidylinositol Phosphate Kinase II Beta
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol Phosphate Kinase II Beta

▶

8. Citations (1)

▶

Unit-cell length a length_a	109.079 Å
Unit-cell length b length_b	186.438 Å
Unit-cell length c length_c	106.326 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	35.687 Å
R factor r_factor	0.2165
R_work r_work	0.2139
R_free r_free	0.2677

fit	/app/data/saxs_computation/em/7em6/7em6.fit
pddf	/app/data/pr_computation/em/7em6/7em6.pr.out
profile	/app/data/saxs_computation/em/7em6/7em6.dat

Crystal structure of the PI5P4Kbeta N203D-ITP complex

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

Phosphatidylinositol 5-phosphate 4-kinase type-2 beta

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