SAXSdb — 2ybx

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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	PHOSPHATE ION × 1 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	2ybx
Deposition date deposition_date	2011-03-30
Structure title title	Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha
Keywords keywords	TRANSFERASE, KINASE, SIGNALLING; 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.

2ybx__assembly_1__model_1

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

Download this curve (.dat)

2ybx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ybx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.18 Å
Rg (electron density)	33.19 Å
Total Rg	33.56 Å
Atom count	5215
Residues	632
Excluded volume	93061 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ybx__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 (3)

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	5362

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	121

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ybxa1
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	d2ybxa2
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	d2ybxb1
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	d2ybxb2
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

CATH v4.4 (4 domains)

Domain ID domain_id	2ybxA01
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	2ybxA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	810 — Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — 2-Layer Sandwich

Domain ID domain_id	2ybxB01
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	2ybxB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	810 — Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — 2-Layer Sandwich

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Unit-cell length a length_a	44.040 Å
Unit-cell length b length_b	98.508 Å
Unit-cell length c length_c	104.879 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.43 °
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	2.560 Å
Low-resolution limit resolution_low	28.370 Å
R factor r_factor	0.1907
R_work r_work	0.1881
R_free r_free	0.2383

Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha

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

2ybx__assembly_1__model_1

2ybx__assembly_1__model_1 | I(q)

2ybx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha

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

2ybx__assembly_1__model_1

2ybx__assembly_1__model_1 | I(q)

2ybx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)