4b2c

Structure of the factor Xa-like trypsin variant triple-Ala (TPA) in complex with eglin C

Method: X-RAY DIFFRACTION Dmax: 109.6 Å Quality: GOOD

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

CATIONIC 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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–246 Mutation:YES EGLIN C × 1 (P01051) CA CALCIUM ION × 1 GOL GLYCEROL × 11 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:283 K;18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.5 AND 100 MM NACL AT 283 K Resolution 1.43 Å R-free 0.182
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–246 Mutation:YES EGLIN C × 1 (P01051) CA CALCIUM ION × 1 GOL GLYCEROL × 9 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:283 K;18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.5 AND 100 MM NACL AT 283 K Resolution 1.43 Å R-free 0.182

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 769 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRY1_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–223; UniProt 24–246 Author chain C; PDBConstruct 1–223; UniProt 24–246

EGLIN C

HIRUDO MEDICINALIS

UniProt P01051

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1–70 Mutation:YES CATIONIC TRYPSIN × 1 (P00760) CA CALCIUM ION × 1 GOL GLYCEROL × 11 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:283 K;18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.5 AND 100 MM NACL AT 283 K Resolution 1.43 Å R-free 0.182
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–70 Mutation:YES CATIONIC TRYPSIN × 1 (P00760) CA CALCIUM ION × 1 GOL GLYCEROL × 9 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:283 K;18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.5 AND 100 MM NACL AT 283 K Resolution 1.43 Å R-free 0.182

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.

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ICIC_HIRME
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–71; UniProt 1–70 Author chain D; PDBConstruct 2–71; UniProt 1–70

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 4b2c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4b2c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4b2c
Deposition date deposition_date2012-07-13
Structure title titleStructure of the factor Xa-like trypsin variant triple-Ala (TPA) in complex with eglin C
Keywords keywordsHYDROLASE-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_guinier32.34
Radius of gyration Rg (electron density) rg_electron32.36
Forward intensity I(0) i069587500.00
Molecular weight molecular_weight65326.0 kDa
Excluded volume excluded_volume81268 ų
Envelope volume envelope_volume101480 ų
Hydration-shell volume shell_volume26853 ų
Envelope diameter envelope_diameter112.8
Shell Rg shell_rg38.07
Envelope Rg envelope_rg32.00
Shape Rg shape_rg32.42
Total Rg total_rg32.64
Total atoms total_atoms4572
Residues n_residues582
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 dmax109.6
Rg (real space) rg_real32.66
Rg uncertainty (real space) rg_real_error1.28
I(0) (real space) i0_real6.9590e+07
I(0) uncertainty (real space) i0_real_error1.1940e+06
Rg (reciprocal space) rg_reciprocal32.53
I(0) (reciprocal space) i0_reciprocal69580000.0000
Solution quality estimate total_estimate0.7969
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.426
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18670000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.655; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.602; Smooth: 0.803

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4b2ca_
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
Domain ID domain_idd4b2cb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.40 — CI-2 family of serine protease inhibitors
Superfamily Superfamily superfamilyd.40.1 — CI-2 family of serine protease inhibitors
Family Family familyd.40.1.1 — CI-2 family of serine protease inhibitors
Domain ID domain_idd4b2cb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4b2cc_
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
Domain ID domain_idd4b2cd1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.40 — CI-2 family of serine protease inhibitors
Superfamily Superfamily superfamilyd.40.1 — CI-2 family of serine protease inhibitors
Family Family familyd.40.1.1 — CI-2 family of serine protease inhibitors
Domain ID domain_idd4b2cd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id4b2cA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4b2cA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4b2cB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology10 — Trypsin Inhibitor V; Chain A
Homologous superfamily homologous superfamily10 — Trypsin Inhibitor V, subunit A
Domain ID domain_id4b2cC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4b2cC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id4b2cD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology10 — Trypsin Inhibitor V; Chain A
Homologous superfamily homologous superfamily10 — Trypsin Inhibitor V, subunit A

8. Citations (1)

9. Files and Curves (10)