3ihy

Human PIK3C3 crystal structure

Method: X-RAY DIFFRACTION

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

Phosphatidylinositol 3-kinase catalytic subunit type 3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PK3C3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–600； UniProt 282–879 Author chain B； PDBConstruct 3–600； UniProt 282–879 Author chain C； PDBConstruct 3–600； UniProt 282–879 Author chain D； PDBConstruct 3–600； UniProt 282–879 Author chain E； PDBConstruct 3–600； UniProt 282–879

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	3ihy
Deposition date deposition_date	2009-07-31
Structure title title	Human PIK3C3 crystal structure
Keywords keywords	;Alpha/Beta protein, Structural Genomics, SGC Stockholm, Structural Genomics Consortium, SGC, ATP-binding, Kinase, Manganese, Nucleotide-binding, Phosphoprotein, 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.

3ihy__assembly_1__model_1

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

Download this curve (.dat)

3ihy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ihy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.97 Å
Rg (electron density)	25.70 Å
Total Rg	26.51 Å
Atom count	4343
Residues	536
Excluded volume	77934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ihy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ihy__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ihy__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ihy__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ihy__assembly_5__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Phosphatidylinositol 3-kinase catalytic subunit type 3
Molecular weight formula_weight	68556.3 kDa
EC 编号 ec_number	2.7.1.137
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	21670

SMSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIH

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ihya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.4 — Phoshoinositide 3-kinase (PI3K), catalytic domain

Domain ID domain_id	d3ihya2
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 (15 domains)

Domain ID domain_id	3ihyA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

Domain ID domain_id	3ihyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	3ihyA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

Domain ID domain_id	3ihyB01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

Domain ID domain_id	3ihyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	3ihyB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

Domain ID domain_id	3ihyC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

Domain ID domain_id	3ihyC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	3ihyC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

Domain ID domain_id	3ihyD01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

Domain ID domain_id	3ihyD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	3ihyD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

Domain ID domain_id	3ihyE01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	70 — Phosphatidylinositol 3-kinase, accessory domain (PIK)

Domain ID domain_id	3ihyE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1010 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4

Domain ID domain_id	3ihyE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1070 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5
Homologous superfamily homologous superfamily	11 — Phosphatidylinositol 3-/4-kinase, catalytic domain

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Unit-cell length a length_a	62.297 Å
Unit-cell length b length_b	96.491 Å
Unit-cell length c length_c	150.679 Å
Unit-cell angle α angle_alpha	107.77 °
Unit-cell angle β angle_beta	91.75 °
Unit-cell angle γ angle_gamma	92.41 °
Molecules per unit cell Z z_pdb	5

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	0.1901
R_work r_work	0.1866
R_free r_free	0.2550

Human PIK3C3 crystal structure

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

Phosphatidylinositol 3-kinase catalytic subunit type 3

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

3ihy__assembly_1__model_1

3ihy__assembly_1__model_1 | I(q)

3ihy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (2 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Human PIK3C3 crystal structure

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

Phosphatidylinositol 3-kinase catalytic subunit type 3

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

3ihy__assembly_1__model_1

3ihy__assembly_1__model_1 | I(q)

3ihy__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (2 domains)

CATH v4.4 (15 domains)

7. Citations (1)