3cvm

High resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form

Method: X-RAY DIFFRACTION Dmax: 91.7 Å Quality: EXCELLENT

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 21–402 Mutation:N150H, K154T, Q319L, M354I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.02 Å R-free 0.282
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–402 Mutation:N150H, K154T, Q319L, M354I No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.02 Å R-free 0.282

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 11–392; UniProt 21–402 Author chain B; PDBConstruct 11–392; UniProt 21–402

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 3cvm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3cvm
Deposition date deposition_date2008-04-18
Structure title titleHigh resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form
Keywords keywords;Plasminogen activator inhibitor type-1, cleaved serpin, Glycoprotein, Plasminogen activation, Polymorphism, Protease inhibitor, Secreted, Serine protease inhibitor, BLOOD CLOTTING ;; BLOOD CLOTTING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.33
Radius of gyration Rg (electron density) rg_electron28.34
Forward intensity I(0) i0109862000.00
Molecular weight molecular_weight85044.0 kDa
Excluded volume excluded_volume107280 ų
Envelope volume envelope_volume127210 ų
Hydration-shell volume shell_volume36819 ų
Envelope diameter envelope_diameter97.9
Shell Rg shell_rg36.15
Envelope Rg envelope_rg28.39
Shape Rg shape_rg28.33
Total Rg total_rg29.09
Total atoms total_atoms11984
Residues n_residues754
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 dmax91.7
Rg (real space) rg_real29.25
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real1.0990e+08
I(0) uncertainty (real space) i0_real_error1.6210e+06
Rg (reciprocal space) rg_reciprocal29.29
I(0) (reciprocal space) i0_reciprocal109900000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.2
Skewness Skewness skewness0.226
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31430000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.945

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cvma_
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_idd3cvmb_
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_id3cvmA01
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_id3cvmA02
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_id3cvmB01
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_id3cvmB02
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)