SAXSdb — 3drg

▼

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

Oligopeptide-binding protein oppA

Lactococcus lactis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Bradykinin × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A2RJ53_LACLM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–578； UniProt 24–600

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	3drg
Deposition date deposition_date	2008-07-11
Structure title title	Lactococcal OppA complexed with bradykinin in the closed conformation
Keywords keywords	oligo-peptide binding, voluminous binding cavity, venus fly-trap, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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.

3drg__assembly_1__model_1

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

Download this curve (.dat)

3drg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3drg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.93 Å
Rg (electron density)	23.97 Å
Total Rg	24.99 Å
Atom count	4442
Residues	571
Excluded volume	78873 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3drg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Oligopeptide-binding protein oppA
Molecular weight formula_weight	65144.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4579

MGSNQSSSTSTKKLKAGNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSSAKLATKGSIEGRHHHHHH

Source Source

Source organism organism	Lactococcus lactis
NCBI taxonomy ID ncbi_taxonomy_id	416870
Host organism host_organism	Lactococcus lactis

Entity 2 Entity 2 polymer

Description description	Bradykinin
Molecular weight formula_weight	976.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RPPGFSPFA

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	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	137

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3drgA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	105 — Dipeptide-binding Protein; domain 3
Homologous superfamily homologous superfamily	10 — Dipeptide-binding Protein; Domain 3

▶

Unit-cell length a length_a	42.175 Å
Unit-cell length b length_b	58.636 Å
Unit-cell length c length_c	61.277 Å
Unit-cell angle α angle_alpha	100.97 °
Unit-cell angle β angle_beta	101.12 °
Unit-cell angle γ angle_gamma	103.02 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	58.320 Å
R factor r_factor	0.2200
R_work r_work	0.2180
R_free r_free	0.2750

Lactococcal OppA complexed with bradykinin in the closed conformation

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

Oligopeptide-binding protein oppA

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

3drg__assembly_1__model_1

3drg__assembly_1__model_1 | I(q)

3drg__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Lactococcal OppA complexed with bradykinin in the closed conformation

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

Oligopeptide-binding protein oppA

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

3drg__assembly_1__model_1

3drg__assembly_1__model_1 | I(q)

3drg__assembly_1__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)