SAXSdb — 1nr5

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

3-DEHYDROQUINATE SYNTHASE

Emericella nidulans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID × 1 COBALT (II) ION × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 [1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID × 2 COBALT (II) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARO1_EMENI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–393； UniProt 1–393 Author chain B； PDBConstruct 1–393； UniProt 1–393

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	1nr5
Deposition date deposition_date	2003-01-23
Structure title title	Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and carbaphosphonate
Keywords keywords	SHIKIMATE PATHWAY, AROMATIC AMINO ACID BIOSYNTHESIS, DHQS, CARBAPHOSPHONATE, CLOSED FORM, DOMAIN MOVEMENT, CYCLASE, LYASE; LYASE
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.

1nr5__assembly_2__model_1

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

Download this curve (.dat)

1nr5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nr5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.78 Å
Rg (electron density)	20.82 Å
Total Rg	21.71 Å
Atom count	3057
Residues	390
Excluded volume	54822 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nr5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nr5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nr5__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	3-DEHYDROQUINATE SYNTHASE
Molecular weight formula_weight	42966.5 kDa
EC 编号 ec_number	4.2.3.4
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	6495

MSNPTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVTPGEHRFEGTEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP

Source Source

Source organism organism	Emericella nidulans
NCBI taxonomy ID ncbi_taxonomy_id	162425
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	2

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
Molecular weight formula_weight	270.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 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	383

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1nr5a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.22 — Dehydroquinate synthase-like
Superfamily Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
Family Family family	e.22.1.1 — Dehydroquinate synthase, DHQS

Domain ID domain_id	d1nr5b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.22 — Dehydroquinate synthase-like
Superfamily Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
Family Family family	e.22.1.1 — Dehydroquinate synthase, DHQS

CATH v4.4 (4 domains)

Domain ID domain_id	1nr5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1nr5A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
Homologous superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

Domain ID domain_id	1nr5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1nr5B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
Homologous superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

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Unit-cell length a length_a	133.990 Å
Unit-cell length b length_b	86.560 Å
Unit-cell length c length_c	74.820 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	27.220 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2320

Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and carbaphosphonate

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

3-DEHYDROQUINATE 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

1nr5__assembly_2__model_1

1nr5__assembly_2__model_1 | I(q)

1nr5__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and carbaphosphonate

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

3-DEHYDROQUINATE 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

1nr5__assembly_2__model_1

1nr5__assembly_2__model_1 | I(q)

1nr5__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 (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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (2)