SAXSdb — 4lv7

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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	INOSITOL HEXAKISPHOSPHATE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ZINC ION × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	INOSITOL HEXAKISPHOSPHATE × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 ZINC ION × 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 35–485； UniProt 1–451 Author chain B； PDBConstruct 35–485； 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	4lv7
Deposition date deposition_date	2013-07-26
Structure title title	Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C
Keywords keywords	transferase, ipk, ins5p 2-k, atipk1, ip5 2-k, inositol phosphorylation; 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.

4lv7__assembly_2__model_1

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

Download this curve (.dat)

4lv7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4lv7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.36 Å
Rg (electron density)	21.50 Å
Total Rg	22.38 Å
Atom count	3201
Residues	394
Excluded volume	57148 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4lv7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4lv7__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Inositol-pentakisphosphate 2-kinase
Molecular weight formula_weight	55321.7 kDa
EC 编号 ec_number	2.7.1.158
Mutation mutation	E82C, S142C
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	6380

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRILMEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNSNGVVSVLTSDEQHLWRENNELISSPNKCVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDCALILNDHSLFSQGITSGGDCISVEIKPKCGFLPTSRFIGKENILKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICKEGRPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAENTAEQIGNSKPSHSDYKDDDDK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress,thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4lv7A01
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

Domain ID domain_id	4lv7B01
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	59.763 Å
Unit-cell length b length_b	59.353 Å
Unit-cell length c length_c	82.232 Å
Unit-cell angle α angle_alpha	83.01 °
Unit-cell angle β angle_beta	89.92 °
Unit-cell angle γ angle_gamma	63.41 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	34.548 Å
R factor r_factor	0.2287
R_work r_work	0.2244
R_free r_free	0.2943

Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C

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

4lv7__assembly_2__model_1

4lv7__assembly_2__model_1 | I(q)

4lv7__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 (5)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C

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

4lv7__assembly_2__model_1

4lv7__assembly_2__model_1 | I(q)

4lv7__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 (5)

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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)