9qdi

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

Method: X-RAY DIFFRACTION

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

Lipoprotein

Bacteroides fragilis NCTC 9343

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Synthetic peptide SER-THR-PRO-PRO × 1 POTASSIUM ION × 2 ZINC ION × 4 1,2-ETHANEDIOL × 4 N-PROPANOL × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Synthetic peptide SER-THR-PRO-PRO × 1 POTASSIUM ION × 2 ZINC ION × 4 1,2-ETHANEDIOL × 3 N-PROPANOL × 1 1,4-BUTANEDIOL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Synthetic peptide SER-THR-PRO-PRO × 1 POTASSIUM ION × 2 ZINC ION × 4 1,2-ETHANEDIOL × 4 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Synthetic peptide SER-THR-PRO-PRO × 1 POTASSIUM ION × 2 ZINC ION × 4 1,2-ETHANEDIOL × 4 N-PROPANOL × 2 HEXANE-1,6-DIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5L9L3_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–409； UniProt 19–426 Author chain B； PDBConstruct 2–409； UniProt 19–426 Author chain C； PDBConstruct 2–409； UniProt 19–426 Author chain D； PDBConstruct 2–409； UniProt 19–426 Author chain E； PDBConstruct 2–409； UniProt 19–426 Author chain F； PDBConstruct 2–409； UniProt 19–426 Author chain G； PDBConstruct 2–409； UniProt 19–426 Author chain H； PDBConstruct 2–409； UniProt 19–426

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	9qdi
Deposition date deposition_date	2025-03-06
Structure title title	Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide
Keywords keywords	;IgA protease, peptidase, protease, BF3526, M64, metallopeptidase, metalloprotease, antibody, Ig, IgA, Bacteroides, metzincin, nephropathy, IgAN, hinge, complex, substrate, product, HYDROLASE ;; HYDROLASE
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.

9qdi__assembly_1__model_1

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

Download this curve (.dat)

9qdi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qdi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.74 Å
Rg (electron density)	29.11 Å
Total Rg	29.85 Å
Atom count	9674
Residues	811
Excluded volume	115560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qdi__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9qdi__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9qdi__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9qdi__assembly_4__model_1`	trimeric （3）	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 (10)

Entity 1 Entity 1 polymer

Description description	Lipoprotein
Molecular weight formula_weight	46148.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	43108

GAQNFSDYFTNKTLRIDYLFTGNADKQSICLDELSELPVWAGRRHHLSELPLEGNGQIVMRDVASGKVIYTTSFSSLFQEWLETDEAKEVTKGFENTYLLPYPIKPAEVEITLRNNKREVSANLKHVVKPDDILIHKKGLTHITPHKYLLKSGNEEQCIDVAILAEGYTTSEMETFYKDAAIACEALFSHEPFQSMKNRFNIVAVASPSADSGVSAPKQGAWKHTAFGSHFDTFYSDRYLTTSRVKAINDALAGIPYEHIIILANTEQYGGGGIYNAFTLTTAHHPNFRPVVVHEFGHSFGGLADEYFYDEDVMNGLYPLNIEPWEQNITTRINFASKWEDMLTKTTPVPTPVADKAKYPIGVYEGGGYSAKGIYRPAFDCRMRTNEYPTFCPVCQRAIQRIIEFYTGK

Source Source

Source organism organism	Bacteroides fragilis NCTC 9343
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Synthetic peptide SER-THR-PRO-PRO
Molecular weight formula_weight	400.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

STPP

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 6 Entity 6 non-polymer

Description description	N-PROPANOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	1,4-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	HEXANE-1,6-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1372

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Unit-cell length a length_a	99.294 Å
Unit-cell length b length_b	99.435 Å
Unit-cell length c length_c	103.386 Å
Unit-cell angle α angle_alpha	74.16 °
Unit-cell angle β angle_beta	88.13 °
Unit-cell angle γ angle_gamma	82.44 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	29.640 Å
R factor r_factor	0.1729
R_work r_work	0.1709
R_free r_free	0.2127

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

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

Lipoprotein

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

9qdi__assembly_1__model_1

9qdi__assembly_1__model_1 | I(q)

9qdi__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 (10)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

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

Lipoprotein

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

9qdi__assembly_1__model_1

9qdi__assembly_1__model_1 | I(q)

9qdi__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 (10)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)