SAXSdb — 2iyo

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

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING

LACTOCOCCUS LACTIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	6-PHOSPHOGLUCONIC ACID × 2 CACODYLATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	6PGD_LACLC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–472； UniProt 1–472

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	2iyo
Deposition date deposition_date	2006-07-21
Structure title title	Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition
Keywords keywords	OXIDOREDUCTASE, 6-PHOSPHOGLUCONATE DEHYDROGENASE, NADP, PENTOSE SHUNT, GLUCONATE UTILIZATION; OXIDOREDUCTASE
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.

2iyo__assembly_1__model_1

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

Download this curve (.dat)

2iyo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2iyo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.22 Å
Rg (electron density)	29.36 Å
Total Rg	30.08 Å
Atom count	7388
Residues	940
Excluded volume	131600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2iyo__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 (4)

Entity 1 Entity 1 polymer

Description description	6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
Molecular weight formula_weight	52501.2 kDa
EC 编号 ec_number	1.1.1.44
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	4007

MAQANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVFKEHQDKNLVFTKTLEEFVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGGNTHFPDTMRRNAELADSGINFIGTGVSGGEKGALLGPSMMPGGQKEAYDLVAPIFEQIAAKAPQDGKPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAESYDLLKRILGLSNAEIQAIFEEWNEGELDSYLIEITKEVLKRKDDEGEGYIVDKILDKAGNKGTGKWTSESALDLGVPLPLITESVFARYISTYKDERVKASKVLSGPALDFSGDKKEVIEKIRKALYFSKIMSYAQGFAQLRKASEEFDWDLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDITKRYQEAVRDVVSLAVQAGTPIPTFTSAISYYDSYRSENLPANLIQAQRDYFGAHTYERTDKAGIFHYDWYTED

Source Source

Source organism organism	LACTOCOCCUS LACTIS
NCBI taxonomy ID ncbi_taxonomy_id	1358
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	6-PHOSPHOGLUCONIC ACID
Molecular weight formula_weight	276.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	313

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2iyoa1
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.2.1.0 — automated matches

Domain ID domain_id	d2iyoa2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2iyoA01
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	2iyoA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1040 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2
Homologous superfamily homologous superfamily	10 — N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2

Domain ID domain_id	2iyoA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	320 — 6-Phosphogluconate Dehydrogenase, domain 3

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Unit-cell length a length_a	60.582 Å
Unit-cell length b length_b	60.582 Å
Unit-cell length c length_c	243.128 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.1620
R_work r_work	0.1590
R_free r_free	0.2210

Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition

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

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING

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

2iyo__assembly_1__model_1

2iyo__assembly_1__model_1 | I(q)

2iyo__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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition

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

6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING

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

2iyo__assembly_1__model_1

2iyo__assembly_1__model_1 | I(q)

2iyo__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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)