SAXSdb — 8ppi

▼

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

Inositol-trisphosphate 3-kinase A

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	;beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate ; × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 3 MANGANESE (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate ; × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 SULFATE ION × 4 MANGANESE (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IP3KA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–279； UniProt 188–461 Author chain B； PDBConstruct 6–279； UniProt 188–461

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	8ppi
Deposition date deposition_date	2023-07-07
Structure title title	Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn
Keywords keywords	Inositol polyphosphate, InsP, inositol kinase, IP3K, calcium, InsP3, IP3, IPK, IP3 3-K, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8ppi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8ppi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ppi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.44 Å
Rg (electron density)	19.21 Å
Total Rg	20.00 Å
Atom count	2270
Residues	273
Excluded volume	39728 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ppi__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8ppi__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Inositol-trisphosphate 3-kinase A
Molecular weight formula_weight	31877.3 kDa
EC 编号 ec_number	2.7.1.127
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	5135

GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER

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	;beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate ;
Molecular weight formula_weight	434.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	472

▶

Unit-cell length a length_a	73.953 Å
Unit-cell length b length_b	98.124 Å
Unit-cell length c length_c	193.163 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	1.650 Å
Low-resolution limit resolution_low	96.580 Å
R factor r_factor	0.1864
R_work r_work	0.1849
R_free r_free	0.2140

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn

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

Inositol-trisphosphate 3-kinase A

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

8ppi__assembly_2__model_1

8ppi__assembly_2__model_1 | I(q)

8ppi__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,1'-trisphosphate/ATP/Mn

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

Inositol-trisphosphate 3-kinase A

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

8ppi__assembly_2__model_1

8ppi__assembly_2__model_1 | I(q)

8ppi__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)