2g5c

Crystal Structure of Prephenate Dehydrogenase from Aquifex aeolicus

Method: X-RAY DIFFRACTION

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

prephenate dehydrogenase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O67636_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–281； UniProt 31–310 Author chain B； PDBConstruct 2–281； UniProt 31–310 Author chain C； PDBConstruct 2–281； UniProt 31–310 Author chain D； PDBConstruct 2–281； UniProt 31–310

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	2g5c
Deposition date deposition_date	2006-02-22
Structure title title	Crystal Structure of Prephenate Dehydrogenase from Aquifex aeolicus
Keywords keywords	prephenate dehydrogenase, TyrA, OXIDOREDUCTASE; 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.

2g5c__assembly_2__model_1

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

Download this curve (.dat)

2g5c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2g5c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.88 Å
Rg (electron density)	28.47 Å
Total Rg	28.97 Å
Atom count	4502
Residues	544
Excluded volume	81208 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2g5c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2g5c__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	prephenate dehydrogenase
Molecular weight formula_weight	31979.7 kDa
EC 编号 ec_number	1.3.1.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9487

MQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	501

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2g5ca1
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.100.1.12 — TyrA dimerization domain-like

Domain ID domain_id	d2g5ca2
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2g5cb1
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.100.1.12 — TyrA dimerization domain-like

Domain ID domain_id	d2g5cb2
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2g5cc1
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.100.1.12 — TyrA dimerization domain-like

Domain ID domain_id	d2g5cc2
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d2g5cd1
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.100.1.12 — TyrA dimerization domain-like

Domain ID domain_id	d2g5cd2
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.2.1.6 — 6-phosphogluconate dehydrogenase-like, N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	2g5cA01
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	2g5cA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3660 — 6-phosphogluconate dehydrogenase C-terminal fold
Homologous superfamily homologous superfamily	10 — 6-phosphogluconate dehydrogenase C-terminal like domain

Domain ID domain_id	2g5cB01
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	2g5cB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3660 — 6-phosphogluconate dehydrogenase C-terminal fold
Homologous superfamily homologous superfamily	10 — 6-phosphogluconate dehydrogenase C-terminal like domain

Domain ID domain_id	2g5cC01
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	2g5cC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3660 — 6-phosphogluconate dehydrogenase C-terminal fold
Homologous superfamily homologous superfamily	10 — 6-phosphogluconate dehydrogenase C-terminal like domain

Domain ID domain_id	2g5cD01
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	2g5cD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3660 — 6-phosphogluconate dehydrogenase C-terminal fold
Homologous superfamily homologous superfamily	10 — 6-phosphogluconate dehydrogenase C-terminal like domain

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Unit-cell length a length_a	42.707 Å
Unit-cell length b length_b	178.952 Å
Unit-cell length c length_c	75.195 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.930 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2610

Crystal Structure of Prephenate Dehydrogenase from Aquifex aeolicus

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

prephenate dehydrogenase

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

2g5c__assembly_2__model_1

2g5c__assembly_2__model_1 | I(q)

2g5c__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Prephenate Dehydrogenase from Aquifex aeolicus

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

prephenate dehydrogenase

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

2g5c__assembly_2__model_1

2g5c__assembly_2__model_1 | I(q)

2g5c__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)