6d6c

The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12

Method: X-RAY DIFFRACTION

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

Transcriptional activator protein LasR

Pseudomonas aeruginosa PAO1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate × 2 HISTIDINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LASR_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–170； UniProt 1–170 Author chain B； PDBConstruct 1–170； UniProt 1–170 Author chain C； PDBConstruct 1–170； UniProt 1–170 Author chain D； PDBConstruct 1–170； UniProt 1–170 Author chain E； PDBConstruct 1–170； UniProt 1–170 Author chain F； PDBConstruct 1–170； UniProt 1–170 Author chain G； PDBConstruct 1–170； UniProt 1–170 Author chain H； PDBConstruct 1–170； UniProt 1–170 Author chain I； PDBConstruct 1–170； UniProt 1–170 Author chain J； PDBConstruct 1–170； UniProt 1–170 Author chain K； PDBConstruct 1–170； UniProt 1–170 Author chain L； PDBConstruct 1–170； UniProt 1–170

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	6d6c
Deposition date deposition_date	2018-04-20
Structure title title	The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12
Keywords keywords	LuxR receptor, signaling protein-agonist complex; signaling protein/agonist
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.

6d6c__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6d6c__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6d6c__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	22.04 Å
Rg (electron density)	20.76 Å
Total Rg	21.53 Å
Atom count	2594
Residues	320
Excluded volume	46107 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6d6c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6d6c__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6d6c__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6d6c__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6d6c__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6d6c__assembly_6__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	Transcriptional activator protein LasR
Molecular weight formula_weight	19008.5 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	17385

MALVDGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLAFEHP

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl 2-methoxybenzoate
Molecular weight formula_weight	564.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	HISTIDINE
Molecular weight formula_weight	156.2 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	1065

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6d6cA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

Domain ID domain_id	6d6cL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	80 — Transcription factor LuxR-like, autoinducer-binding domain

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Unit-cell length a length_a	54.409 Å
Unit-cell length b length_b	85.341 Å
Unit-cell length c length_c	232.465 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	230.940 Å
R factor r_factor	0.1875
R_work r_work	0.1852
R_free r_free	0.2315

The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12

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

Transcriptional activator protein LasR

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

6d6c__assembly_6__model_1

6d6c__assembly_6__model_1 | I(q)

6d6c__assembly_6__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 12

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

Transcriptional activator protein LasR

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

6d6c__assembly_6__model_1

6d6c__assembly_6__model_1 | I(q)

6d6c__assembly_6__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)