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4dy0

Crystal structure of native protease nexin-1 with heparin

Method: X-RAY DIFFRACTION Dmax: 92.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glia-derived nexin

Homo sapiens

UniProt P07093

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 Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 20–398 Not recorded 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；25mM NaAc, 12% PEG3350, 0.2M (NH4)2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.35 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 20–398 Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；25mM NaAc, 12% PEG3350, 0.2M (NH4)2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.35 Å R-free 0.226
3 Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 20–398 Chain B； UniProt 20–398 Not recorded 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；25mM NaAc, 12% PEG3350, 0.2M (NH4)2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.35 Å R-free 0.226
4 Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 20–398 Chain B； UniProt 20–398 Not recorded 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；25mM NaAc, 12% PEG3350, 0.2M (NH4)2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.35 Å R-free 0.226

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 4DY0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4DY7 Crystal structures of protease nexin-1 in complex with S195A thrombin Deposited 2012-02-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 20–398（379 aa）
Not recorded ACT ACETATE ION × 3 CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；295 K；0.14M calcium acetate, 13% PEG3350, pH 7.4, VAPOR DIFFUSION, temperature 295K
Resolution 2.80 Å R-free 0.268
4DY7 Crystal structures of protease nexin-1 in complex with S195A thrombin Deposited 2012-02-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 20–398（379 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.4；295 K；0.14M calcium acetate, 13% PEG3350, pH 7.4, VAPOR DIFFUSION, temperature 295K
Resolution 2.80 Å R-free 0.268

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GDN_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–379； UniProt 20–398 Author chain B； PDBConstruct 1–379； UniProt 20–398

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4dy0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4dy0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4dy0
Deposition date deposition_date2012-02-28
Structure title titleCrystal structure of native protease nexin-1 with heparin
Keywords keywordsserpin, protease inhibitor, thrombin, cell surface, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.43 Å
Radius of gyration Rg (electron density) rg_electron28.23 Å
Forward intensity I(0) i098538400.00
Molecular weight molecular_weight80329.0 kDa
Excluded volume excluded_volume101470 ų
Envelope volume envelope_volume122060 ų
Hydration-shell volume shell_volume35355 ų
Envelope diameter envelope_diameter96.6 Å
Shell Rg shell_rg36.20 Å
Envelope Rg envelope_rg28.19 Å
Shape Rg shape_rg28.21 Å
Total Rg total_rg29.05 Å
Total atoms total_atoms5647
Residues n_residues732
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.0 Å
Rg (real space) rg_real29.33 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real9.8540e+07
I(0) uncertainty (real space) i0_real_error1.3880e+06
Rg (reciprocal space) rg_reciprocal29.37 Å
I(0) (reciprocal space) i0_reciprocal98540000.0000
Solution quality estimate total_estimate0.9077
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.4 Å
Skewness Skewness skewness0.168
Kurtosis Kurtosis kurtosis-0.621
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28870000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.967
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4dy0a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.0 — automated matches
Domain ID domain_idd4dy0b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4dy0A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id4dy0A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
Domain ID domain_id4dy0B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily10 — Antithrombin, subunit I, domain 2
Domain ID domain_id4dy0B02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1
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8. Citations (1)

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9. Files and Curves (10)