4pyo

Humanized rat COMT bound to SAH, semi-holo form

Method: X-RAY DIFFRACTION Dmax: 78.2 Å Quality: EXCELLENT

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

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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 44–264 Mutation:M134I, Y138C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:293 K;VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.10 Å R-free 0.233
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 44–264 Mutation:M134I, Y138C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:293 K;VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.10 Å R-free 0.233

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 159 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 1–221; UniProt 44–264 Author chain B; PDBConstruct 1–221; UniProt 44–264

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 4pyo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4pyo
Deposition date deposition_date2014-03-27
Structure title titleHumanized rat COMT bound to SAH, semi-holo form
Keywords keywords;METHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, ALTERNATIVE INITIATION, CATECHOLAMINE METABOLISM, CELL MEMBRANE, MEMBRANE, METAL-BINDING, PHOSPHOPROTEIN, SIGNAL-ANCHOR, TRANSMEMBRANE ANCHOR, ENZYME MECHANISM, CONFORMATIONAL CHANGE, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.61
Radius of gyration Rg (electron density) rg_electron23.82
Forward intensity I(0) i039293900.00
Molecular weight molecular_weight48778.0 kDa
Excluded volume excluded_volume61226 ų
Envelope volume envelope_volume71952 ų
Hydration-shell volume shell_volume25414 ų
Envelope diameter envelope_diameter79.9
Shell Rg shell_rg30.57
Envelope Rg envelope_rg23.77
Shape Rg shape_rg23.83
Total Rg total_rg24.58
Total atoms total_atoms3416
Residues n_residues429
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 dmax78.2
Rg (real space) rg_real24.58
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real3.9290e+07
I(0) uncertainty (real space) i0_real_error5.4760e+05
Rg (reciprocal space) rg_reciprocal24.59
I(0) (reciprocal space) i0_reciprocal39290000.0000
Solution quality estimate total_estimate0.9020
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.549
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14370000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4pyoa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.1 — COMT-like
Domain ID domain_idd4pyob_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.1 — COMT-like

CATH v4.4 (2 domains)

Domain ID domain_id4pyoA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id4pyoB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39

8. Citations (1)

9. Files and Curves (10)