SAXSdb — 1lq8

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

plasma serine protease inhibitor

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 30–375 Chain B； UniProt 376–406	Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Fragment：C-terminal fragment from elastase cleavage, residues 376-405	2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2	Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 30–375 Chain D； UniProt 376–406	Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Fragment：C-terminal fragment from elastase cleavage, residues 376-405	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 30–375 Chain F； UniProt 376–406	Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Fragment：C-terminal fragment from elastase cleavage, residues 376-405	No other associated polymer	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
4	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 30–375 Chain H； UniProt 376–406	Fragment：N-terminal fragment from elastase cleavage, residues 30-375 Fragment：C-terminal fragment from elastase cleavage, residues 376-405	2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose × 1 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

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 1LQ8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HI9 Crystal Structure of human native protein C inhibitor Deposited 2006-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 44–406（363 aa） Fragment：residues 25-387 Chain B 44–406（363 aa） Fragment：residues 25-387 Chain C 44–406（363 aa） Fragment：residues 25-387	Not recorded	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
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 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 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IPSP_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–346； UniProt 30–375 Author chain C； PDBConstruct 1–346； UniProt 30–375 Author chain E； PDBConstruct 1–346； UniProt 30–375 Author chain G； PDBConstruct 1–346； UniProt 30–375 Author chain B； PDBConstruct 1–31； UniProt 376–406 Author chain D； PDBConstruct 1–31； UniProt 376–406 Author chain F； PDBConstruct 1–31； UniProt 376–406 Author chain H； PDBConstruct 1–31； UniProt 376–406

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	1lq8
Deposition date deposition_date	2002-05-09
Structure title title	Crystal structure of cleaved protein C inhibitor
Keywords keywords	serpin, protease, inhibitor, heparin, retinoic acid, protein C, BLOOD CLOTTING; BLOOD CLOTTING
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	43.40 Å
Radius of gyration Rg (electron density) rg_electron	43.04 Å
Forward intensity I(0) i0	385081000.00
Molecular weight molecular_weight	164270.0 kDa
Excluded volume excluded_volume	207120 Å³
Envelope volume envelope_volume	274830 Å³
Hydration-shell volume shell_volume	54290 Å³
Envelope diameter envelope_diameter	147.7 Å
Shell Rg shell_rg	46.46 Å
Envelope Rg envelope_rg	42.53 Å
Shape Rg shape_rg	43.03 Å
Total Rg total_rg	43.24 Å
Total atoms total_atoms	11559
Residues n_residues	1431
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	151.4 Å
Rg (real space) rg_real	43.52 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	3.8510e+08
I(0) uncertainty (real space) i0_real_error	7.2160e+06
Rg (reciprocal space) rg_reciprocal	43.41 Å
I(0) (reciprocal space) i0_reciprocal	385000000.0000
Solution quality estimate total_estimate	0.8696
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.7 Å
Skewness Skewness skewness	0.377
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	54800000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.901

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	plasma serine protease inhibitor
Molecular weight formula_weight	38651.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	11658

RVEDLHVGATVAPSSRRDFTFDLYRALASAAPSQNIFFSPVSISMSLAMLSLGAGSSTKMQILEGLGLNLQKSSEKELHRGFQQLLQELNQPRDGFQLSLGNALFTDLVVDLQDTFVSAMKTLYLADTFPTNFRDSAGAMKQINDYVAKQTKGKIVDLLKNLDSNAVVIMVNYIFFKAKWETSFNHKGTQEQDFYVTSETVVRVPMMSREDQYHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQQVENGLSEKTLRKWLKMFKKRQLELYLPKFSIEGSYQLEKVLPSLGISNVFTSHADLSGISNHSNIQVSEMVHKAVVEVDESGTRAAAATGTIFTFRSA

Entity 2 Entity 2 polymer

Description description	plasma serine protease inhibitor
Molecular weight formula_weight	3737.4 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

RLNSQRLVFNRPFLMFIVDNNILFLGKVNRP

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 branched

Description description	alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	3

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1lq8.1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

Domain ID domain_id	d1lq8.2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

Domain ID domain_id	d1lq8.3
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

Domain ID domain_id	d1lq8.4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

CATH v4.4 (8 domains)

Domain ID domain_id	1lq8A01
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	1lq8A02
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	1lq8C01
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	1lq8C02
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	1lq8E01
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	1lq8E02
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	1lq8G01
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	1lq8G02
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

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8. Citations (1)

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Unit-cell length a length_a	55.200 Å
Unit-cell length b length_b	244.030 Å
Unit-cell length c length_c	66.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	45.660 Å
R factor r_factor	—
R_work r_work	0.2220
R_free r_free	0.2790

fit	/app/data/saxs_computation/lq/1lq8/1lq8.fit
pddf	/app/data/pr_computation/lq/1lq8/1lq8.pr.out
profile	/app/data/saxs_computation/lq/1lq8/1lq8.dat

Crystal structure of cleaved 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

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)