5lqu

Crystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-5-[6-(ethylamino)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide

Method: X-RAY DIFFRACTION Dmax: 76.4 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 Fragment:SOLUBLE FORM, RESIDUES 44-264 619 N-[(E)-3-[(2R,3S,4R,5R)-5-(6-ethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;295 K;AMMONIUM SULPHATE, CHES, PH 9 Resolution 1.80 Å R-free 0.205
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 44–264 Fragment:SOLUBLE FORM, RESIDUES 44-264 619 N-[(E)-3-[(2R,3S,4R,5R)-5-(6-ethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;295 K;AMMONIUM SULPHATE, CHES, PH 9 Resolution 1.80 Å R-free 0.205

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 5lqu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lqu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lqu
Deposition date deposition_date2016-08-17
Structure title titleCrystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-5-[6-(ethylamino)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide
Keywords keywordsMETHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.04
Radius of gyration Rg (electron density) rg_electron23.29
Forward intensity I(0) i039765200.00
Molecular weight molecular_weight49394.0 kDa
Excluded volume excluded_volume62023 ų
Envelope volume envelope_volume71354 ų
Hydration-shell volume shell_volume25620 ų
Envelope diameter envelope_diameter79.8
Shell Rg shell_rg30.14
Envelope Rg envelope_rg23.25
Shape Rg shape_rg23.28
Total Rg total_rg24.08
Total atoms total_atoms3461
Residues n_residues427
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 dmax76.4
Rg (real space) rg_real23.99
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real3.9770e+07
I(0) uncertainty (real space) i0_real_error5.3460e+05
Rg (reciprocal space) rg_reciprocal24.00
I(0) (reciprocal space) i0_reciprocal39770000.0000
Solution quality estimate total_estimate0.9035
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.3
Skewness Skewness skewness0.264
Kurtosis Kurtosis kurtosis-0.531
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11650000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5lqua_
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_idd5lqub_
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_id5lquA00
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_id5lquB00
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)