SAXSdb — 6ym3

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

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid × 2 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PI42A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–394； UniProt 35–405 Author chain B； PDBConstruct 24–394； UniProt 35–405

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6ym3
Deposition date deposition_date	2020-04-07
Structure title title	Crystal structure of Compound 1 with PIP4K2A
Keywords keywords	PIP4K2A, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6ym3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ym3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ym3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.12 Å
Rg (electron density)	33.10 Å
Total Rg	33.50 Å
Atom count	5245
Residues	624
Excluded volume	93656 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ym3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Molecular weight formula_weight	45313.0 kDa
EC 编号 ec_number	2.7.1.149
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	5415

MHHHHHHSSGVDLGTENLYFQSMDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVECEENDGEEEGESDGTHPVGTPPDSPGNTLNSSPPLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFLDFIGHIL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid
Molecular weight formula_weight	440.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6ym3a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.143 — SAICAR synthase-like
Superfamily Superfamily superfamily	d.143.1 — SAICAR synthase-like
Family Family family	d.143.1.2 — Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta

Domain ID domain_id	d6ym3a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6ym3b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.143 — SAICAR synthase-like
Superfamily Superfamily superfamily	d.143.1 — SAICAR synthase-like
Family Family family	d.143.1.2 — Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta

Domain ID domain_id	d6ym3b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	43.934 Å
Unit-cell length b length_b	98.132 Å
Unit-cell length c length_c	104.256 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	45.990 Å
R factor r_factor	0.2036
R_work r_work	0.2019
R_free r_free	0.2500

Crystal structure of Compound 1 with PIP4K2A

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

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ym3__assembly_1__model_1

6ym3__assembly_1__model_1 | I(q)

6ym3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of Compound 1 with PIP4K2A

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

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ym3__assembly_1__model_1

6ym3__assembly_1__model_1 | I(q)

6ym3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)