SAXSdb — 3qhy

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

Beta-lactamase

Bacillus anthracis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 39–309	Fragment：unp residues 39-309	Beta-lactamase inhibitory protein II × 1 （O87916）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；298 K；0.1M Bicine, 13 % PEG 10,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.06 Å R-free 0.217

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q93T42_BACAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 39–309

Beta-lactamase inhibitory protein II

Streptomyces exfoliatus

UniProt O87916

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 41–311	Fragment：unp residues 41-311	Beta-lactamase × 1 （Q93T42）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；298 K；0.1M Bicine, 13 % PEG 10,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.06 Å R-free 0.217

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3QHY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JTD Crystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase Deposited 2001-08-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 39–311（273 aa）	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG8000, calcium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.230
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 41–311（271 aa） Fragment：unp residues 41-311 Chain B 41–311（271 aa） Fragment：unp residues 41-311 Chain C 41–311（271 aa） Fragment：unp residues 41-311 Chain D 41–311（271 aa） Fragment：unp residues 41-311 Chain E 41–311（271 aa） Fragment：unp residues 41-311 Chain F 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 35	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 41–311（271 aa） Fragment：unp residues 41-311 Chain F 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 41–311（271 aa） Fragment：unp residues 41-311 Chain C 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3QI0 Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases Deposited 2011-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 41–311（271 aa） Fragment：unp residues 41-311 Chain E 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	SO4 SULFATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
9T9P Adenosine receptor A2a (A2AR)-beta-lactamase fusion bound to beta-lactamase inhibitory protein II (BLIPII) and ZM241385 Deposited 2025-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 41–311（271 aa）	Not recorded	ZMA 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

3 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O87916_STREX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–271； UniProt 41–311

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	3qhy
Deposition date deposition_date	2011-01-26
Structure title title	Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases
Keywords keywords	enyzme-inhibitor complex, beta-propeller, beta-lactamase, protein:protein interaction, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.35 Å
Radius of gyration Rg (electron density) rg_electron	23.52 Å
Forward intensity I(0) i0	52225700.00
Molecular weight molecular_weight	55366.0 kDa
Excluded volume excluded_volume	68962 Å³
Envelope volume envelope_volume	79567 Å³
Hydration-shell volume shell_volume	27993 Å³
Envelope diameter envelope_diameter	78.5 Å
Shell Rg shell_rg	30.93 Å
Envelope Rg envelope_rg	23.65 Å
Shape Rg shape_rg	23.47 Å
Total Rg total_rg	24.47 Å
Total atoms total_atoms	3910
Residues n_residues	529
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	77.5 Å
Rg (real space) rg_real	24.30 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	5.2230e+07
I(0) uncertainty (real space) i0_real_error	7.1440e+05
Rg (reciprocal space) rg_reciprocal	24.31 Å
I(0) (reciprocal space) i0_reciprocal	52230000.0000
Solution quality estimate total_estimate	0.8918
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.327
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14680000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.926

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
Molecular weight formula_weight	29759.6 kDa
EC 编号 ec_number	3.5.2.6
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	4418

KEKTGQVKHKNQATHKEFSQLEKKFDARLGVYAIDTGTNQTIAYRPNERFAFASTYKALAAGVLLQQNSTKKLDEVITYTKEDLVDYSPVTEKHVDTGMTLGEIAEAAVRYSDNTAGNILFHKIGGPKGYEKALRQMGDRVTMSDRFETELNEAIPGDIRDTSTAKAIATNLKAFTAGNALPNHKRNILTKWMKGNATGDKLIRAGVPTNWVVADKSGAGSYGTRNDIAIVWPPNRAPIIIAILSSKDEKGATYDNQLIAEAAEVIVNAFR

来源 Source

来源生物 organism	Bacillus anthracis
通用名 common_name	anthrax,anthrax bacterium
NCBI Class编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-lactamase inhibitory protein II
Molecular weight formula_weight	28360.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ATSVVAWGGNNDWGEATVPAEAQSGVDAIAGGYFHGLALKGGKVLGWGANLNGQLTMPAATQSGVDAIAAGNYHSLALKDGEVIAWGGNEDGQTTVPAEARSGVDAIAAGAWASYALKDGKVIAWGDDSDGQTTVPAEAQSGVTALDGGVYTALAVKNGGVIAWGDNYFGQTTVPAEAQSGVDDVAGGIFHSLALKDGKVIAWGDNRYKQTTVPTEALSGVSAIASGEWYSLALKNGKVIAWGSSRTAPSSVQSGVSSIEAGPNAAYALKGGSGSGHHHHHH

来源 Source

来源生物 organism	Streptomyces exfoliatus
通用名 common_name	Streptomyces hydrogenans
NCBI Class编号 ncbi_taxonomy_id	1905
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	508

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3qhya_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d3qhyb_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

CATH v4.4 (2 domains)

Domain ID domain_id	3qhyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	3qhyB00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

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8. Citations (1)

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Unit-cell length a length_a	130.766 Å
Unit-cell length b length_b	87.177 Å
Unit-cell length c length_c	61.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.060 Å
Low-resolution limit resolution_low	49.950 Å
R factor r_factor	0.1720
R_work r_work	0.1690
R_free r_free	0.2170

fit	/app/data/saxs_computation/qh/3qhy/3qhy.fit
pddf	/app/data/pr_computation/qh/3qhy/3qhy.pr.out
profile	/app/data/saxs_computation/qh/3qhy/3qhy.dat

Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases

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

Beta-lactamase

State in the Current Structure

Other States of the Same Protein in the Database

Beta-lactamase inhibitory protein II

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)