SAXSdb — 2hi9

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

Plasma serine protease inhibitor

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 44–406 Chain B； UniProt 44–406 Chain C； UniProt 44–406	Fragment：residues 25-387	CIT CITRIC ACID × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；66.7mM tri-potassium citrate, 6.7% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.30 Å R-free 0.269

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 2HI9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LQ8 Crystal structure of cleaved protein C inhibitor Deposited 2002-05-09	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 30–375（346 aa） Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Chain B 376–406（31 aa） Fragment：C-terminal fragment from elastase cleavage, residues 376-405	Not recorded	IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, sodium fluoride, isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.40 Å R-free 0.279
1LQ8 Crystal structure of cleaved protein C inhibitor Deposited 2002-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 30–375（346 aa） Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Chain D 376–406（31 aa） Fragment：C-terminal fragment from elastase cleavage, residues 376-405	Not recorded	IPA ISOPROPYL ALCOHOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, sodium fluoride, isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.40 Å R-free 0.279
1LQ8 Crystal structure of cleaved protein C inhibitor Deposited 2002-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 30–375（346 aa） Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Chain F 376–406（31 aa） Fragment：C-terminal fragment from elastase cleavage, residues 376-405	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, sodium fluoride, isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.40 Å R-free 0.279
1LQ8 Crystal structure of cleaved protein C inhibitor Deposited 2002-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 30–375（346 aa） Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Chain H 376–406（31 aa） Fragment：C-terminal fragment from elastase cleavage, residues 376-405	Not recorded	IPA ISOPROPYL ALCOHOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 3350, sodium fluoride, isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.40 Å R-free 0.279
2OL2 High Resolution Structure of Native PCI in Space Group P21 Deposited 2007-01-18	Different construct Different mutation/modification 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 36–406（371 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；6% PEG 3350, 0.04M ammonium citrate,10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.271
2OL2 High Resolution Structure of Native PCI in Space Group P21 Deposited 2007-01-18	Different construct Different mutation/modification 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 36–406（371 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；6% PEG 3350, 0.04M ammonium citrate,10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.271
3B9F 1.6 A structure of the PCI-thrombin-heparin complex Deposited 2007-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 36–406（371 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；11% PEG 3350, 0.12M MgSO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.234
3DY0 Crystal Structure of Cleaved PCI Bound to Heparin Deposited 2008-07-25	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 37–372（336 aa） Fragment：PPE cleaved, residues 37-372 Chain B 379–406（28 aa） Fragment：PPE cleaved, residues 379-406	Not recorded	NO3 NITRATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；0.12M Lithium Nitrate, 12% PEG 3350, 25% Glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.55 Å R-free 0.217

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IPSP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–363； UniProt 44–406 Author chain B； PDBConstruct 1–363； UniProt 44–406 Author chain C； PDBConstruct 1–363； UniProt 44–406

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	2hi9
Deposition date deposition_date	2006-06-29
Structure title title	Crystal Structure of human native protein C inhibitor
Keywords keywords	;Serpin, coagulation, haemostasis, thrombin inhibitor, activated protein C inhibitor, acrosin inhibitor, serine protease inhibitor, HYDROLASE inhibitor ;; 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	36.51 Å
Radius of gyration Rg (electron density) rg_electron	35.81 Å
Forward intensity I(0) i0	208055000.00
Molecular weight molecular_weight	118080.0 kDa
Excluded volume excluded_volume	148600 Å³
Envelope volume envelope_volume	195390 Å³
Hydration-shell volume shell_volume	46151 Å³
Envelope diameter envelope_diameter	131.1 Å
Shell Rg shell_rg	41.27 Å
Envelope Rg envelope_rg	35.64 Å
Shape Rg shape_rg	35.79 Å
Total Rg total_rg	36.24 Å
Total atoms total_atoms	8315
Residues n_residues	1056
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	122.3 Å
Rg (real space) rg_real	36.57 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	2.0810e+08
I(0) uncertainty (real space) i0_real_error	3.7320e+06
Rg (reciprocal space) rg_reciprocal	36.53 Å
I(0) (reciprocal space) i0_reciprocal	208000000.0000
Solution quality estimate total_estimate	0.8634
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.415
Kurtosis Kurtosis kurtosis	-0.086
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	49240000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.737

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Plasma serine protease inhibitor
Molecular weight formula_weight	40935.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	8785

SRRDFTFDLYRALASAAPSQNIFFSPVSISMSLAMLSLGAGSSTKMQILEGLGLNLQKSSEKELHRGFQQLLQELNQPRDGFQLSLGNALFTDLVVDLQDTFVSAMKTLYLADTFPTNFRDSAGAMKQINDYVAKQTKGKIVDLLKNLDSNAVVIMVNYIFFKAKWETSFNHKGTQEQDFYVTSETVVRVPMMSREDQYHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQQVENGLSEKTLRKWLKMFKKRQLELYLPKFSIEGSYQLEKVLPSLGISNVFTSHADLSGISNHSNIQVSEMVHKAVVEVDESGTRAAAATGTIFTFRSARLNSQRLVFNRPFLMFIVDNNILFLGKVNRP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	382

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2hi9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	2hi9A02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

Domain ID domain_id	2hi9B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	2hi9B02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

Domain ID domain_id	2hi9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	2hi9C02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

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8. Citations (1)

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Unit-cell length a length_a	198.590 Å
Unit-cell length b length_b	70.950 Å
Unit-cell length c length_c	123.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2690

fit	/app/data/saxs_computation/hi/2hi9/2hi9.fit
pddf	/app/data/pr_computation/hi/2hi9/2hi9.pr.out
profile	/app/data/saxs_computation/hi/2hi9/2hi9.dat

Crystal Structure of human native protein C inhibitor

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

Plasma serine protease inhibitor

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