3nwb

Rat COMT in complex with a fluorinated desoxyribose-containing bisubstrate inhibitor avoids hydroxyl group

Method: X-RAY DIFFRACTION Dmax: 55.3 Å Quality: REASONABLE

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 Fragment:soluble form, UNP residues 44-264 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 659 N-[(E)-3-[(2R,3R,4S,5R)-3-fluoro-4-hydroxy-5-[6-(methylamino)purin-9-yl]oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;300 K;ammonium sulphate, ches, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 300K Resolution 1.30 Å R-free 0.164

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 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 3nwb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3nwb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3nwb
Deposition date deposition_date2010-07-09
Structure title titleRat COMT in complex with a fluorinated desoxyribose-containing bisubstrate inhibitor avoids hydroxyl group
Keywords keywords;METHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, ALTERNATIVE INITIATION, CATECHOLAMINE METABOLISM, CELL MEMBRANE, MAGNESIUM, MEMBRANE, METAL-BINDING, PHOSPHOPROTEIN, S-ADENOSYL-L-METHIONINE, SIGNAL-ANCHOR, TRANSMEMBRANE, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.54
Radius of gyration Rg (electron density) rg_electron16.38
Forward intensity I(0) i011061700.00
Molecular weight molecular_weight24908.0 kDa
Excluded volume excluded_volume31174 ų
Envelope volume envelope_volume33936 ų
Hydration-shell volume shell_volume17064 ų
Envelope diameter envelope_diameter56.2
Shell Rg shell_rg22.86
Envelope Rg envelope_rg16.73
Shape Rg shape_rg16.37
Total Rg total_rg17.41
Total atoms total_atoms3461
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 dmax55.3
Rg (real space) rg_real17.43
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.1060e+07
I(0) uncertainty (real space) i0_real_error1.1490e+05
Rg (reciprocal space) rg_reciprocal17.44
I(0) (reciprocal space) i0_reciprocal11060000.0000
Solution quality estimate total_estimate0.6306
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.4
Skewness Skewness skewness0.179
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2799000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 0.998; Sysdev: 0.242; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3nwba_
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 (1 domains)

Domain ID domain_id3nwbA00
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)