SAXSdb — 3hk3

▼

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

Thrombin light chain

Mus musculus

UniProt P19221

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 317–360 Chain B； UniProt 361–618	Fragment：Light chain: UNP residues 317-360 Fragment：Heavy chain: UNP residues 361-618 Mutation：W215A, E217A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；295 K；200mM Ammonium chloride, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.94 Å R-free 0.235

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 3HK3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OCV Structural basis of Na+ activation mimicry in murine thrombin Deposited 2006-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 319–360（42 aa） Chain B 361–618（258 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50	Resolution 2.20 Å R-free 0.246
2OCV Structural basis of Na+ activation mimicry in murine thrombin Deposited 2006-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 319–360（42 aa） Chain B 361–618（258 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50	Resolution 2.20 Å R-free 0.246
2PUX Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR3 Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 317–360（44 aa） Chain B 361–618（258 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；20% PEG 10000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.225
2PV9 Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4 Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 317–360（44 aa） Chain B 361–618（258 aa）	Mutation：S195A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；20% PEG 3350, 200 mM MgSO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.50 Å R-free 0.319
2PV9 Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4 Deposited 2007-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 317–360（44 aa） Chain B 361–618（258 aa）	Mutation：S195A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；20% PEG 3350, 200 mM MgSO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.50 Å R-free 0.319
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 317–360（44 aa） Chain B 361–618（258 aa）	Mutation：W215A, E217A	SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.243
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 317–360（44 aa） Chain D 361–618（258 aa）	Mutation：W215A, E217A	SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.243
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 317–360（44 aa） Chain F 361–618（258 aa）	Mutation：W215A, E217A	SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.40 Å R-free 0.243
3HK6 Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit) Deposited 2009-05-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 317–360（44 aa） Fragment：Light chain: UNP residues 317-360 Chain B 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618	Mutation：W215A, E217A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；200mM Ammonium dihydrogen phosphate, 14% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.314
3HK6 Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit) Deposited 2009-05-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 317–360（44 aa） Fragment：Light chain: UNP residues 317-360 Chain D 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618	Mutation：W215A, E217A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；200mM Ammonium dihydrogen phosphate, 14% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.20 Å R-free 0.314
3HKI Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 317–360（44 aa） Fragment：Light chain: UNP residues 317-360 Chain B 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618	Mutation：W215A, E217A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM Tris-HCl pH 8.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.261
3HKI Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 317–360（44 aa） Fragment：Light chain: UNP residues 317-360 Chain E 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618	Mutation：W215A, E217A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM Tris-HCl pH 8.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.261

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

View Construct and Data Evidence

UniProt name	THRB_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–44； UniProt 317–360 Author chain B； PDBConstruct 1–258； UniProt 361–618

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	3hk3
Deposition date deposition_date	2009-05-22
Structure title title	Crystal structure of murine thrombin mutant W215A/E217A (one molecule in the asymmetric unit)
Keywords keywords	;Serine protease, Acute phase, Blood coagulation, Calcium, Cleavage on pair of basic residues, Disulfide bond, Gamma-carboxyglutamic acid, Glycoprotein, Hydrolase, Kringle, Protease, Zymogen ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	18.97 Å
Radius of gyration Rg (electron density) rg_electron	17.77 Å
Forward intensity I(0) i0	17901200.00
Molecular weight molecular_weight	32488.0 kDa
Excluded volume excluded_volume	40910 Å³
Envelope volume envelope_volume	46382 Å³
Hydration-shell volume shell_volume	20896 Å³
Envelope diameter envelope_diameter	60.0 Å
Shell Rg shell_rg	24.87 Å
Envelope Rg envelope_rg	18.16 Å
Shape Rg shape_rg	17.76 Å
Total Rg total_rg	18.83 Å
Total atoms total_atoms	2288
Residues n_residues	243
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

▼

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

Maximum dimension Dmax dmax	59.4 Å
Rg (real space) rg_real	18.81 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	1.7900e+07
I(0) uncertainty (real space) i0_real_error	2.0840e+05
Rg (reciprocal space) rg_reciprocal	18.83 Å
I(0) (reciprocal space) i0_reciprocal	17900000.0000
Solution quality estimate total_estimate	0.8879
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.078
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7702000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.984

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Thrombin light chain
Molecular weight formula_weight	5105.7 kDa
EC 编号 ec_number	3.4.21.5
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	2528

FHTFFNEKTFGLGEADCGLRPLFEKKSLKDTTEKELLDSYIDGR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Thrombin heavy chain
Molecular weight formula_weight	29795.5 kDa
EC 编号 ec_number	3.4.21.5
Mutation mutation	W215A, E217A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IVEGWDAEKGIAPWQVMLFRKSPQELLCGASLISDRWVLTAAHCILYPPWDKNFTENDLLVRIGKHSRTRYERNVEKISMLEKIYVHPRYNWRENLDRDIALLKLKKPVPFSDYIHPVCLPDKQTVTSLLRAGYKGRVTGWGNLRETWTTNINEIQPSVLQVVNLPIVERPVCKASTRIRITDNMFCAGFKVNDTKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSAGAGCDRKGKYGFYTHVFRLKRWIQKVIDQFG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	240

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3hk3B01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	3hk3B02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

▶

8. Citations (2)

▶

Unit-cell length a length_a	48.647 Å
Unit-cell length b length_b	63.939 Å
Unit-cell length c length_c	95.024 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	43.310 Å
R factor r_factor	0.1834
R_work r_work	0.1807
R_free r_free	0.2354

fit	/app/data/saxs_computation/hk/3hk3/3hk3.fit
pddf	/app/data/pr_computation/hk/3hk3/3hk3.pr.out
profile	/app/data/saxs_computation/hk/3hk3/3hk3.dat

Crystal structure of murine thrombin mutant W215A/E217A (one molecule in the asymmetric unit)

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

Thrombin light chain

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) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)