3n86

Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4

Method: X-RAY DIFFRACTION

▼

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

3-dehydroquinate dehydratase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	(1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid × 12 water × 12	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	(1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AROQ_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–147； UniProt 1–147 Author chain B； PDBConstruct 1–147； UniProt 1–147 Author chain C； PDBConstruct 1–147； UniProt 1–147 Author chain D； PDBConstruct 1–147； UniProt 1–147 Author chain E； PDBConstruct 1–147； UniProt 1–147 Author chain F； PDBConstruct 1–147； UniProt 1–147 Author chain G； PDBConstruct 1–147； UniProt 1–147 Author chain H； PDBConstruct 1–147； UniProt 1–147 Author chain I； PDBConstruct 1–147； UniProt 1–147 Author chain J； PDBConstruct 1–147； UniProt 1–147 Author chain K； PDBConstruct 1–147； UniProt 1–147 Author chain L； PDBConstruct 1–147； UniProt 1–147 Author chain M； PDBConstruct 1–147； UniProt 1–147 Author chain N； PDBConstruct 1–147； UniProt 1–147 Author chain O； PDBConstruct 1–147； UniProt 1–147 Author chain P； PDBConstruct 1–147； UniProt 1–147 Author chain Q； PDBConstruct 1–147； UniProt 1–147 Author chain R； PDBConstruct 1–147； UniProt 1–147 Author chain S； PDBConstruct 1–147； UniProt 1–147 Author chain T； PDBConstruct 1–147； UniProt 1–147 Author chain U； PDBConstruct 1–147； UniProt 1–147 Author chain V； PDBConstruct 1–147； UniProt 1–147 Author chain W； PDBConstruct 1–147； UniProt 1–147 Author chain X； PDBConstruct 1–147； UniProt 1–147

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3n86
Deposition date deposition_date	2010-05-27
Structure title title	Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4
Keywords keywords	;dehydroquinate dehydratase, aroD, Mycobacterium tuberculosis, shikimate pathway, drug discovery, LYASE, LYASE-LYASE INHIBITOR complex ;; LYASE/LYASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3n86__assembly_2__model_1

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

Download this curve (.dat)

3n86__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3n86__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.89 Å
Rg (electron density)	35.10 Å
Total Rg	35.80 Å
Atom count	13177
Residues	1699
Excluded volume	233740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3n86__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3n86__assembly_2__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	3-dehydroquinate dehydratase
Molecular weight formula_weight	15807.9 kDa
Source method src_method	man
Copy count entity_count	24

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Atom count atom_count	30436

MSELIVNVINGPNLGRLGRREPAVYGGTTHDELVALIEREAAELGLKAVVRQSDSEAQLLDWIHQAADAAEPVILNAGGLTHTSVALRDACAELSAPLIEVHISNVHAREEFRRHSYLSPIATGVIVGLGIQGYLLALRYLAEHVGT

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid
Molecular weight formula_weight	319.3 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4105

▼

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d3n86a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86m_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86n_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86o_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86p_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86q_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86r_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86s_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86t_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86u_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86v_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86w_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

Domain ID domain_id	d3n86x_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.13 — Type II 3-dehydroquinate dehydratase
Family Family family	c.23.13.1 — Type II 3-dehydroquinate dehydratase

CATH v4.4 (24 domains)

Domain ID domain_id	3n86A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86J00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86K00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86L00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86M00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86N00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86O00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86P00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86Q00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86R00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86S00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86T00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86U00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86V00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86W00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

Domain ID domain_id	3n86X00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	9100 — Dehydroquinase, class II

▶

Unit-cell length a length_a	91.240 Å
Unit-cell length b length_b	143.976 Å
Unit-cell length c length_c	148.628 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	48

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	56.500 Å
R factor r_factor	0.1583
R_work r_work	0.1555
R_free r_free	0.2120

Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4

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

3-dehydroquinate dehydratase

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

3n86__assembly_2__model_1

3n86__assembly_2__model_1 | I(q)

3n86__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4

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

3-dehydroquinate dehydratase

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

3n86__assembly_2__model_1

3n86__assembly_2__model_1 | I(q)

3n86__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)