2d26

Active site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex

Method: X-RAY DIFFRACTION Dmax: 93.1 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 25–382 Chain B; UniProt 383–418 Fragment:residues 1-358 Fragment:residues 359-394 Elastase-1 × 1 (P00772) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.1;291 K;PEG3350, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.30 Å R-free 0.312

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 1–358; UniProt 25–382 Author chain B; PDBConstruct 1–36; UniProt 383–418

Elastase-1

OrganismNot specified

UniProt P00772

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 27–266 Not recorded Alpha-1-antitrypsin × 1 (P01009) Alpha-1-antitrypsin × 1 (P01009) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.1;291 K;PEG3350, pH 8.10, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.30 Å R-free 0.312

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.

126 other PDB entries and 131 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ELA1_PIG
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–240; UniProt 27–266

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 2d26

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d26
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2d26
Deposition date deposition_date2005-09-03
Structure title titleActive site distortion is sufficient for proteinase inhibit second crystal structure of covalent serpin-proteinase complex
Keywords keywordsSERPINE PROTEINASE, SERPIN, COVALENT SERPIN-PROTEINASE COMP PROTEIN-PROTEIN INTERACTIONS, 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_guinier29.10
Radius of gyration Rg (electron density) rg_electron28.60
Forward intensity I(0) i057216800.00
Molecular weight molecular_weight58040.0 kDa
Excluded volume excluded_volume71903 ų
Envelope volume envelope_volume92914 ų
Hydration-shell volume shell_volume28537 ų
Envelope diameter envelope_diameter98.1
Shell Rg shell_rg34.37
Envelope Rg envelope_rg28.37
Shape Rg shape_rg28.58
Total Rg total_rg29.24
Total atoms total_atoms4114
Residues n_residues579
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 dmax93.1
Rg (real space) rg_real29.25
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real5.7220e+07
I(0) uncertainty (real space) i0_real_error9.5120e+05
Rg (reciprocal space) rg_reciprocal29.19
I(0) (reciprocal space) i0_reciprocal57210000.0000
Solution quality estimate total_estimate0.8632
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.6
Skewness Skewness skewness0.467
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.2700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18090000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.717

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_idd2d26a1
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_idd2d26c1
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 (4 domains)

Domain ID domain_id2d26A01
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_id2d26A02
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_id2d26C01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2d26C02
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)