5p9n

humanized rat COMT in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[[3-[hydroxy-(1-methylindazol-5-yl)methyl]phenyl]methyl]benzamide at 1.17A

Method: X-RAY DIFFRACTION Dmax: 65.9 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, RESIDUES 44-264 Mutation:M134I, Y138C MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 D1D (4S,5S)-1,2-DITHIANE-4,5-DIOL × 1 SO4 SULFATE ION × 1 7JE 5-(4-fluorophenyl)-~{N}-[[3-[(~{R})-(1-methylindazol-5-yl)-oxidanyl-methyl]phenyl]methyl]-2,3-bis(oxidanyl)benzamide × 1 8JE 5-(4-fluorophenyl)-~{N}-[[3-[(~{S})-(1-methylindazol-5-yl)-oxidanyl-methyl]phenyl]methyl]-2,3-bis(oxidanyl)benzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;295 K;AMMONIUM SULPHATE, CHES, PH 9 Resolution 1.17 Å R-free 0.180

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 5p9n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5p9n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5p9n
Deposition date deposition_date2016-10-19
Structure title titlehumanized rat COMT in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[[3-[hydroxy-(1-methylindazol-5-yl)methyl]phenyl]methyl]benzamide at 1.17A
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_guinier17.54
Radius of gyration Rg (electron density) rg_electron16.37
Forward intensity I(0) i010956600.00
Molecular weight molecular_weight24906.0 kDa
Excluded volume excluded_volume31234 ų
Envelope volume envelope_volume33694 ų
Hydration-shell volume shell_volume16992 ų
Envelope diameter envelope_diameter55.6
Shell Rg shell_rg22.83
Envelope Rg envelope_rg16.68
Shape Rg shape_rg16.36
Total Rg total_rg17.39
Total atoms total_atoms1739
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 dmax65.9
Rg (real space) rg_real17.43
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real1.0960e+07
I(0) uncertainty (real space) i0_real_error1.4500e+05
Rg (reciprocal space) rg_reciprocal17.44
I(0) (reciprocal space) i0_reciprocal10960000.0000
Solution quality estimate total_estimate0.7229
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.9
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.4550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3172000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.491; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5p9na_
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_id5p9nA00
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)