SAXSdb — 6uqd

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

Streptopain

Streptococcus pyogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPEB_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–372； UniProt 28–398 Author chain B； PDBConstruct 2–372； UniProt 28–398

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	6uqd
Deposition date deposition_date	2019-10-18
Structure title title	Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor
Keywords keywords	speb, streptopain, inhibitor, nitrile, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

6uqd__assembly_1__model_1

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

Download this curve (.dat)

6uqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6uqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.56 Å
Rg (electron density)	17.46 Å
Total Rg	18.43 Å
Atom count	1939
Residues	247
Excluded volume	33905 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6uqd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6uqd__assembly_2__model_1`	monomeric （1）	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	Streptopain
Molecular weight formula_weight	41551.9 kDa
EC 编号 ec_number	3.4.22.10
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4319

MDQNFARNEKEAKDSAITFIQKSAAIKAGARSAEDIKLDKVNLGGELSGSNMYVYNISTGGFVIVSGDKRSPEILGYSTSGSFDANGKENIASFMESYVEQIKENKKLDTTYAGTAEIKQPVVKSLLNSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKPLEHHHHHH

Source Source

Source organism organism	Streptococcus pyogenes
NCBI taxonomy ID ncbi_taxonomy_id	1314
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate
Molecular weight formula_weight	487.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	385

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Unit-cell length a length_a	45.624 Å
Unit-cell length b length_b	115.516 Å
Unit-cell length c length_c	50.265 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.020 Å
Low-resolution limit resolution_low	43.070 Å
R factor r_factor	0.2170
R_work r_work	0.2150
R_free r_free	0.2570

Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor

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

Streptopain

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

6uqd__assembly_1__model_1

6uqd__assembly_1__model_1 | I(q)

6uqd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)

Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor

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

Streptopain

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

6uqd__assembly_1__model_1

6uqd__assembly_1__model_1 | I(q)

6uqd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Citations (1)