4g8r

Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1

Method: X-RAY DIFFRACTION Dmax: 97.5 Å Quality: REASONABLE

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 28–402 Fragment:UNP residues 28-402 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;298 K;0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K Resolution 2.19 Å R-free 0.215
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 28–402 Fragment:UNP residues 28-402 SO4 SULFATE ION × 1 96P (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate) × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;298 K;0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K Resolution 2.19 Å R-free 0.215

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 54 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 2–376; UniProt 28–402 Author chain B; PDBConstruct 2–376; UniProt 28–402

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 4g8r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4g8r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4g8r
Deposition date deposition_date2012-07-23
Structure title titleCrystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1
Keywords keywordsSERPIN, PAI-1, INHIBITOR, BLOOD CLOTTING, BLOOD CLOTTING-INHIBITOR complex; BLOOD CLOTTING/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.93
Radius of gyration Rg (electron density) rg_electron29.04
Forward intensity I(0) i0104259000.00
Molecular weight molecular_weight82653.0 kDa
Excluded volume excluded_volume104190 ų
Envelope volume envelope_volume126530 ų
Hydration-shell volume shell_volume36291 ų
Envelope diameter envelope_diameter104.5
Shell Rg shell_rg36.40
Envelope Rg envelope_rg29.11
Shape Rg shape_rg29.03
Total Rg total_rg29.74
Total atoms total_atoms5826
Residues n_residues725
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 dmax97.5
Rg (real space) rg_real29.91
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real1.0430e+08
I(0) uncertainty (real space) i0_real_error1.4770e+06
Rg (reciprocal space) rg_reciprocal29.92
I(0) (reciprocal space) i0_reciprocal104300000.0000
Solution quality estimate total_estimate0.6914
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.3
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.385
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39480000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.996; Smooth: 0.910

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4g8ra_
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_idd4g8rb1
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_idd4g8rb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4g8rA01
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_id4g8rA02
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_id4g8rB01
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_id4g8rB02
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)