SAXSdb — 4axf

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

INOSITOL-PENTAKISPHOSPHATE 2-KINASE

ARABIDOPSIS THALIANA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 Myo inositol 3,4,5,6 tetrakisphosphate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPPK_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–456； UniProt 1–451

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	4axf
Deposition date deposition_date	2012-06-12
Structure title title	InsP5 2-K in complex with Ins(3,4,5,6)P4 plus AMPPNP
Keywords keywords	TRANSFERASE, INOSITOL KINASE, PHYTIC ACID, PROTEIN KINASE, INOSITIDE 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.

4axf__assembly_1__model_1

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

Download this curve (.dat)

4axf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4axf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.02 Å
Rg (electron density)	22.10 Å
Total Rg	23.01 Å
Atom count	3320
Residues	410
Excluded volume	59137 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4axf__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	INOSITOL-PENTAKISPHOSPHATE 2-KINASE
Molecular weight formula_weight	51321.2 kDa
EC 编号 ec_number	2.7.1.158
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3320

GEFELMEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNSNGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGITSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICREGRPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAENTAEQIGNSKPSHS

Source Source

Source organism organism	ARABIDOPSIS THALIANA
Common name common_name	THALE CRESS
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	Myo inositol 3,4,5,6 tetrakisphosphate
Molecular weight formula_weight	500.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4axfA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	110 — Inositol-pentakisphosphate 2-kinase, N-lobe

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Unit-cell length a length_a	61.620 Å
Unit-cell length b length_b	65.080 Å
Unit-cell length c length_c	122.490 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.930 Å
Low-resolution limit resolution_low	57.420 Å
R factor r_factor	0.2272
R_work r_work	0.2246
R_free r_free	0.2792

InsP5 2-K in complex with Ins(3,4,5,6)P4 plus AMPPNP

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

INOSITOL-PENTAKISPHOSPHATE 2-KINASE

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

4axf__assembly_1__model_1

4axf__assembly_1__model_1 | I(q)

4axf__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 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

InsP5 2-K in complex with Ins(3,4,5,6)P4 plus AMPPNP

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

INOSITOL-PENTAKISPHOSPHATE 2-KINASE

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

4axf__assembly_1__model_1

4axf__assembly_1__model_1 | I(q)

4axf__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 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)