SAXSdb — 2x6h

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

PHOSPHOTIDYLINOSITOL 3 KINASE 59F

DROSOPHILA MELANOGASTER

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9W1M7_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–696； UniProt 258–949 Author chain B； PDBConstruct 5–696； UniProt 258–949

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	2x6h
Deposition date deposition_date	2010-02-17
Structure title title	THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34
Keywords keywords	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.

2x6h__assembly_1__model_1

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

Download this curve (.dat)

2x6h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2x6h__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.66 Å
Rg (electron density)	39.81 Å
Total Rg	39.97 Å
Atom count	8886
Residues	1086
Excluded volume	159980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2x6h__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 (2)

Entity 1 Entity 1 polymer

Description description	PHOSPHOTIDYLINOSITOL 3 KINASE 59F
Molecular weight formula_weight	78765.5 kDa
EC 编号 ec_number	2.7.1.137, 2.7.1.153, 2.7.1.154
Mutation mutation	YES
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	8916

GSHMDSEIQMENLVERKHHRLARSERSGISDRDAKPTASIRDQLHTIVYRYPPTYVLSSEEQDLVWKFRFYLSSHKKALTKFLKCINWKLEDEVTQALWMLANWAPMDVEDALELLSPTFTHPQVRKYAVSRLAQAPDEDLLLYLLQLVQALKYEDPRHIVHLHGCIFPERDVVRSILDDNGSLLDQSSLSDLSATSSGLHASVIPANQRAASVLAAIKSDKSVSPGSAGGSGSGGQGSVALPNPSAPATPGSSSLPCDSNSNALMLAEGISFGSVPANLCTFLIQRACTNATLANYFYWYLSIEVEEVESVRKQDERAHDMYAMVLKMFLKVLENGNFNLRGIFYNLRKQRRFIDELVKLVKLVAKEPGNRNKKTEKFQKLLAEQDMFKVNFTNFEPIPFPLDPEIYITKIVPMRTSLFKSALMPAKLTFVTSIAHHEYAAIFKHGDDLRQDQLILQMITLMDKLLRRENLDLKLTPYKVLATSSKHGFLQYVDSCTVAEVLAREGNIHNFFRKHHPCDNGPYGISAEVMDTYIKSCAGYCVITYLLGVGDRHLDNLLLTTNGKLFHIDFGYILGRDPKPMPPPMKLSKEMVEAMGGISSEHHHEFRKQCYTAYLHLRRHANVMLNLFSLMVDATVPDIALEPDKAVKKVEENLQLGLTDEEAVQHLQSLLDVSITAVMPALVEQIHRFTQYWRK

Source Source

Source organism organism	DROSOPHILA MELANOGASTER
Common name common_name	FRUIT FLY
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2x6hA01
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	2x6hA02
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	2x6hA03
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	2x6hB01
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	2x6hB02
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	2x6hB03
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	110.600 Å
Unit-cell length b length_b	154.790 Å
Unit-cell length c length_c	243.080 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	72.360 Å
R factor r_factor	0.2420
R_work r_work	0.2400
R_free r_free	0.2780

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34

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

PHOSPHOTIDYLINOSITOL 3 KINASE 59F

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

2x6h__assembly_1__model_1

2x6h__assembly_1__model_1 | I(q)

2x6h__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34

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

PHOSPHOTIDYLINOSITOL 3 KINASE 59F

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

2x6h__assembly_1__model_1

2x6h__assembly_1__model_1 | I(q)

2x6h__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)