1ezx

CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX

Method: X-RAY DIFFRACTION Dmax: 95.0 Å Quality: GOOD

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

ALPHA-1-ANTITRYPSIN

Homo sapiens

UniProt P01009

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 48–382 Chain B; UniProt 383–418 Fragment:N-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359 Fragment:C-TERMINAL FRAGMENT OF PROTEOLYTIC CLEAVAGE AT MET358-SER359 TRYPSIN × 1 (P00760) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;PEG 3350, sodium citrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.60 Å R-free 0.239

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.

45 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A1AT_HUMAN
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 1–335; UniProt 48–382 Author chain B; PDBConstruct 1–36; UniProt 383–418

TRYPSIN

Bos taurus

UniProt P00760

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–243 Not recorded ALPHA-1-ANTITRYPSIN × 1 (P01009) ALPHA-1-ANTITRYPSIN × 1 (P01009) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277 K;PEG 3350, sodium citrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.60 Å R-free 0.239

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.

608 other PDB entries and 770 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY1_BOVIN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 45–243; UniProt 1–243

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 1ezx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ezx
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1ezx
Deposition date deposition_date2000-05-12
Structure title titleCRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX
Keywords keywordsprotease-inhibitor complex, serpin, alpha-1-antitrypsin, trypsin, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.70
Radius of gyration Rg (electron density) rg_electron27.06
Forward intensity I(0) i048585800.00
Molecular weight molecular_weight55499.0 kDa
Excluded volume excluded_volume69942 ų
Envelope volume envelope_volume85553 ų
Hydration-shell volume shell_volume27758 ų
Envelope diameter envelope_diameter97.8
Shell Rg shell_rg33.01
Envelope Rg envelope_rg27.19
Shape Rg shape_rg27.00
Total Rg total_rg27.88
Total atoms total_atoms3903
Residues n_residues511
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 dmax95.0
Rg (real space) rg_real27.87
Rg uncertainty (real space) rg_real_error0.69
I(0) (real space) i0_real4.8590e+07
I(0) uncertainty (real space) i0_real_error6.8480e+05
Rg (reciprocal space) rg_reciprocal27.82
I(0) (reciprocal space) i0_reciprocal48580000.0000
Solution quality estimate total_estimate0.8568
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.505
Kurtosis Kurtosis kurtosis-0.242
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10430000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.892; Smooth: 0.904

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ezx.1
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_idd1ezxc_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases

CATH v4.4 (3 domains)

Domain ID domain_id1ezxA01
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_id1ezxA02
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_id1ezxC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases

8. Citations (1)

9. Files and Curves (10)