2ntf

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog

Method: X-RAY DIFFRACTION

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

Murine Antibody Fab RS2-1G9 Lambda Light Chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 1 （Q99LC4） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 1 （Q99LC4） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain × 2 （Q99LC4） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0VDX6_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 20–230 Author chain L； PDBConstruct 1–211； UniProt 20–230

Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain

OrganismNot specified

UniProt Q99LC4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 1 （Q0VDX6） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 1 （Q0VDX6） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Murine Antibody Fab RS2-1G9 Lambda Light Chain × 2 （Q0VDX6） 3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q99LC4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–222； UniProt 20–239 Author chain H； PDBConstruct 1–222； UniProt 20–239

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	2ntf
Deposition date deposition_date	2006-11-07
Structure title title	Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog
Keywords keywords	Immunoglobulin, antibody, Fab, hapten complex, quorum sensing, homoserine lactone, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

2ntf__assembly_2__model_1

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

Download this curve (.dat)

2ntf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ntf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.94 Å
Rg (electron density)	23.98 Å
Total Rg	24.85 Å
Atom count	3326
Residues	433
Excluded volume	58884 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ntf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ntf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ntf__assembly_3__model_1`	tetrameric （4）	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	Murine Antibody Fab RS2-1G9 Lambda Light Chain
Molecular weight formula_weight	22840.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,A
Atom count atom_count	6652

QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAGAWERHSSYSCQVTHEGHTVEKSLSR

Entity 2 Entity 2 polymer

Description description	Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain
Molecular weight formula_weight	24082.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B

QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR

Entity 3 Entity 3 non-polymer

Description description	3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE
Molecular weight formula_weight	296.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2ntfa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfa2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2ntfb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ntfl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	2ntfA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ntfL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	118.659 Å
Unit-cell length b length_b	118.659 Å
Unit-cell length c length_c	176.042 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	44.020 Å
R factor r_factor	0.2130
R_work r_work	0.2100
R_free r_free	0.2650

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog

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

Murine Antibody Fab RS2-1G9 Lambda Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain

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

2ntf__assembly_2__model_1

2ntf__assembly_2__model_1 | I(q)

2ntf__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog

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

Murine Antibody Fab RS2-1G9 Lambda Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Murine Antibody Fab RS2-1G9 IGG1 Heavy Chain

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

2ntf__assembly_2__model_1

2ntf__assembly_2__model_1 | I(q)

2ntf__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)