SAXSdb — 1vko

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

inositol-3-phosphate synthase

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	POTASSIUM ION × 4 CHLORIDE ION × 8 IODIDE ION × 8 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 PYROPHOSPHATE 2- × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q18664_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–537； UniProt 1–525

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	1vko
Deposition date deposition_date	2004-06-11
Structure title title	Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution
Keywords keywords	;ce21227, INOSITOL-3-PHOSPHATE SYNTHASE, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, ISOMERASE ;; ISOMERASE
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.

1vko__assembly_1__model_1

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

Download this curve (.dat)

1vko__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vko__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.90 Å
Rg (electron density)	38.25 Å
Total Rg	38.55 Å
Atom count	16260
Residues	2044
Excluded volume	289390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vko__assembly_1__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	inositol-3-phosphate synthase
Molecular weight formula_weight	60006.8 kDa
EC 编号 ec_number	5.5.1.4
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	4217

MGSDKIHHHHHHMSSAQVNGISKRLIVESPNVKLEDGVLESRFTYRKNHFEHRADGLHVTPKEHDYSFKTVLKPRKTGLLLVGLGGNNGSTAVGSIFANQYAMTWRTKEGHSQANYFGSVTQTATVHLGYDSATQNQIFVPFKDIVPILSPNDLIISGWDISDSNLYEAMGRAKVFEPELQEKLRPFMEPIVPLPSIYYPDFIASNQGDRANNVIPGDNKLEHLEHIRADIRKFKQEHELECVIVLWTANTERYTDVRQGLNATADEIMESIRVNEDEVSPSNIFAVASILEGAHYINGSPQNTLVPGLIELAERHKVFVGGDDFKSGQTKFKSAFVDFLVSSGMKPESIVSYNHLGNNDGKNLSEARQFRSKEISKSSVVDDMVKSNQILFPDAKNPDYCVVIKYVPYVADSKRAMDEYICSIFMGGKQTFVVHNTCEDSLLASPLIYDLAILTELASRVSYKVDDEYKPFHSVLSILSLLLKAPVVPPGTPISNAFMRQFSTLTKLVTALAGFPSDTDMQIEFFTQLPAAKSKSQ

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vkoa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1vkoa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.3 — Dihydrodipicolinate reductase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1vkoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1vkoA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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Unit-cell length a length_a	76.980 Å
Unit-cell length b length_b	129.980 Å
Unit-cell length c length_c	131.320 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.410 Å
R factor r_factor	0.2035
R_work r_work	0.2004
R_free r_free	0.2646

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

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

inositol-3-phosphate synthase

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

1vko__assembly_1__model_1

1vko__assembly_1__model_1 | I(q)

1vko__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of inositol-3-phosphate synthase (ce21227) from Caenorhabditis elegans at 2.30 A resolution

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

inositol-3-phosphate synthase

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

1vko__assembly_1__model_1

1vko__assembly_1__model_1 | I(q)

1vko__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)