6lfe

Rat-COMT, Nitecapone,SAM and Mg bond

Method: X-RAY DIFFRACTION Dmax: 55.8 Å Quality: GOOD

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 Not recorded SAM S-ADENOSYLMETHIONINE × 1 EAO 3-(3,4-dihydroxy-5-nitrobenzylidene)pentane-2,4-dione × 1 MG MAGNESIUM ION × 1 IPA ISOPROPYL ALCOHOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.1M HEPES sodium pH 7.5 10%v/v 2-propanol 20%w/v polyethylene glycol 4000 Resolution 1.60 Å R-free 0.166

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 3–223; 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 6lfe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6lfe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6lfe
Deposition date deposition_date2019-12-02
Structure title titleRat-COMT, Nitecapone,SAM and Mg bond
Keywords keywordsEnzyme S-adenosylmethionone catechol, catecholamine, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.33
Radius of gyration Rg (electron density) rg_electron16.23
Forward intensity I(0) i010803400.00
Molecular weight molecular_weight24866.0 kDa
Excluded volume excluded_volume31241 ų
Envelope volume envelope_volume33489 ų
Hydration-shell volume shell_volume16968 ų
Envelope diameter envelope_diameter55.6
Shell Rg shell_rg22.70
Envelope Rg envelope_rg16.58
Shape Rg shape_rg16.24
Total Rg total_rg17.21
Total atoms total_atoms1742
Residues n_residues213
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 dmax55.8
Rg (real space) rg_real17.22
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.0800e+07
I(0) uncertainty (real space) i0_real_error1.1760e+05
Rg (reciprocal space) rg_reciprocal17.23
I(0) (reciprocal space) i0_reciprocal10800000.0000
Solution quality estimate total_estimate0.8022
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.8
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.304
Angular range angular_range— – 0.4600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3035000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6lfea_
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

8. Citations (1)

9. Files and Curves (10)