3q03

Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation.

Method: X-RAY DIFFRACTION Dmax: 103.7 Å Quality: GOOD

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

Plasminogen activator inhibitor 1

Homo sapiens

UniProt P05121

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 24–402 Mutation:W175F ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.1;293 K;1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.64 Å R-free 0.225
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 24–402 Mutation:W175F ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.1;293 K;1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.64 Å R-free 0.225
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–402 Chain B; UniProt 24–402 Mutation:W175F ZN ZINC ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.1;293 K;1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.64 Å R-free 0.225

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.

28 other PDB entries and 53 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAI1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–379; UniProt 24–402 Author chain B; PDBConstruct 1–379; UniProt 24–402

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 3q03

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3q03
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3q03
Deposition date deposition_date2010-12-15
Structure title titleCrystal structure of plasminogen activator inhibitor-1 in a metastable active conformation.
Keywords keywordsPAI-1, active serpin, serine protease inhibitor, metastable conformation, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.22
Radius of gyration Rg (electron density) rg_electron30.62
Forward intensity I(0) i0102987000.00
Molecular weight molecular_weight82334.0 kDa
Excluded volume excluded_volume103710 ų
Envelope volume envelope_volume123870 ų
Hydration-shell volume shell_volume34612 ų
Envelope diameter envelope_diameter109.9
Shell Rg shell_rg36.61
Envelope Rg envelope_rg30.80
Shape Rg shape_rg30.62
Total Rg total_rg31.13
Total atoms total_atoms5793
Residues n_residues724
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax103.7
Rg (real space) rg_real31.35
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real1.0300e+08
I(0) uncertainty (real space) i0_real_error1.5950e+06
Rg (reciprocal space) rg_reciprocal31.30
I(0) (reciprocal space) i0_reciprocal103000000.0000
Solution quality estimate total_estimate0.8618
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.5
Skewness Skewness skewness0.455
Kurtosis Kurtosis kurtosis-0.263
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35630000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.738

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3q03a_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins
Domain ID domain_idd3q03b_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins

CATH v4.4 (4 domains)

Domain ID domain_id3q03A01
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_id3q03A02
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_id3q03B01
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_id3q03B02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily10 — Alpha-1-antitrypsin, domain 1

8. Citations (1)

9. Files and Curves (10)