7ud6

Designed Enzyme SH3-588 (Catechol O-methyltransferase catalytic domain and Src homology 3 binding domain fusion)

Method: X-RAY DIFFRACTION Dmax: 75.3 Å Quality: REASONABLE

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

Tyrosine-protein kinase Fyn,Catechol O-methyltransferase

Rattus norvegicus

UniProt E5RFS5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 86–141 Mutation:Q26V,N29R,E37L,R39V,R73E,Y74F,Q77L,N78V,T93Q,Q97Y,K98R SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;297 K;0.7 M magnesium formate, 0.1 M bis-tris propone pH 7.0. Resolution 2.59 Å R-free 0.278

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E5RFS5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–57; UniProt 86–141

Tyrosine-protein kinase Fyn,Catechol O-methyltransferase

Rattus norvegicus

UniProt P22734

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 47–258 Mutation:Q26V,N29R,E37L,R39V,R73E,Y74F,Q77L,N78V,T93Q,Q97Y,K98R SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;297 K;0.7 M magnesium formate, 0.1 M bis-tris propone pH 7.0. Resolution 2.59 Å R-free 0.278

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.

96 other PDB entries and 160 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COMT_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 66–277; UniProt 47–258

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 7ud6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ud6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ud6
Deposition date deposition_date2022-03-18
Structure title titleDesigned Enzyme SH3-588 (Catechol O-methyltransferase catalytic domain and Src homology 3 binding domain fusion)
Keywords keywordsDesigned enzyme, COMT, SH3, fusion protein, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.57
Radius of gyration Rg (electron density) rg_electron21.06
Forward intensity I(0) i014969000.00
Molecular weight molecular_weight29833.0 kDa
Excluded volume excluded_volume37551 ų
Envelope volume envelope_volume42771 ų
Hydration-shell volume shell_volume18194 ų
Envelope diameter envelope_diameter76.0
Shell Rg shell_rg26.41
Envelope Rg envelope_rg21.50
Shape Rg shape_rg21.13
Total Rg total_rg21.58
Total atoms total_atoms2096
Residues n_residues265
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 dmax75.3
Rg (real space) rg_real21.77
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real1.4970e+07
I(0) uncertainty (real space) i0_real_error1.8430e+05
Rg (reciprocal space) rg_reciprocal21.73
I(0) (reciprocal space) i0_reciprocal14970000.0000
Solution quality estimate total_estimate0.6591
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.1
Skewness Skewness skewness0.604
Kurtosis Kurtosis kurtosis-0.090
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3886000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.798; Smooth: 0.955

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)