1ct4

CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-VAL18I IN COMPLEX WITH SGPB

Method: X-RAY DIFFRACTION Dmax: 59.9 Å Quality: REASONABLE

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

PROTEINASE B

OrganismNot specified

UniProt P00777

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 E; UniProt 115–299 Not recorded OVOMUCOID INHIBITOR × 1 (P68390) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.1;298 K;PEG 4000 sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.60 Å

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.

27 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRTB_STRGR
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–185; UniProt 115–299

OVOMUCOID INHIBITOR

Meleagris gallopavo

UniProt P68390

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 I; UniProt 135–185 Fragment:THIRD DOMAIN OMTKY3-VAL18I Mutation:DEL 1-5, L18V PROTEINASE B × 1 (P00777) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.1;298 K;PEG 4000 sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.60 Å

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.

36 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IOVO_MELGA
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–51; UniProt 135–185

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 1ct4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ct4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ct4
Deposition date deposition_date1999-08-18
Structure title titleCRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-VAL18I IN COMPLEX WITH SGPB
Keywords keywordsENZYME-INHIBITOR COMPLEX, BETA-BRANCHED P1 RESIDUE, 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_guinier17.87
Radius of gyration Rg (electron density) rg_electron16.98
Forward intensity I(0) i012031500.00
Molecular weight molecular_weight24220.0 kDa
Excluded volume excluded_volume29540 ų
Envelope volume envelope_volume33264 ų
Hydration-shell volume shell_volume16527 ų
Envelope diameter envelope_diameter61.5
Shell Rg shell_rg23.12
Envelope Rg envelope_rg17.30
Shape Rg shape_rg16.95
Total Rg total_rg17.93
Total atoms total_atoms1696
Residues n_residues236
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 dmax59.9
Rg (real space) rg_real18.28
Rg uncertainty (real space) rg_real_error0.14
I(0) (real space) i0_real1.1920e+07
I(0) uncertainty (real space) i0_real_error1.1360e+05
Rg (reciprocal space) rg_reciprocal17.81
I(0) (reciprocal space) i0_reciprocal12030000.0000
Solution quality estimate total_estimate0.6654
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.9
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis0.001
Angular range angular_range— – 0.4450 −1
Current regularization parameter α current_alpha7.0220
Highest regularization parameter α highest_alpha2816000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.819; Stabil: 0.922; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.461

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ct4e_
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.47.1.1 — Prokaryotic proteases
Domain ID domain_idd1ct4i_
Class classg — Small proteins
Fold Fold foldg.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamilyg.68.1 — Kazal-type serine protease inhibitors
Family Family familyg.68.1.1 — Ovomucoid domain III-like

CATH v4.4 (3 domains)

Domain ID domain_id1ct4E01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ct4E02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ct4I00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30

8. Citations (1)

9. Files and Curves (10)