5p9u

humanized rat catechol O-methyltransferase in complex with SAH and 6-bromo-8-hydroxy-3H-quinazolin-4-one

Method: X-RAY DIFFRACTION Dmax: 49.6 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 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 7JL 6-bromanyl-8-oxidanyl-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;295 K;AMMONIUM SULPHATE, CHES, PH 9 Resolution 1.42 Å R-free 0.243
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 44–264 Fragment:SOLUBLE FORM, RESIDUES 44-264 Mutation:M134I, Y138C MG MAGNESIUM ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 7JL 6-bromanyl-8-oxidanyl-3~{H}-quinazolin-4-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 9;295 K;AMMONIUM SULPHATE, CHES, PH 9 Resolution 1.42 Å R-free 0.243

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

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 5p9u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5p9u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5p9u
Deposition date deposition_date2016-10-19
Structure title titlehumanized rat catechol O-methyltransferase in complex with SAH and 6-bromo-8-hydroxy-3H-quinazolin-4-one
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_guinier19.27
Radius of gyration Rg (electron density) rg_electron18.99
Forward intensity I(0) i010984200.00
Molecular weight molecular_weight24594.0 kDa
Excluded volume excluded_volume30758 ų
Envelope volume envelope_volume37473 ų
Hydration-shell volume shell_volume17339 ų
Envelope diameter envelope_diameter85.0
Shell Rg shell_rg24.15
Envelope Rg envelope_rg21.43
Shape Rg shape_rg19.03
Total Rg total_rg19.64
Total atoms total_atoms1719
Residues n_residues214
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 dmax49.6
Rg (real space) rg_real17.44
Rg uncertainty (real space) rg_real_error0.06
I(0) (real space) i0_real1.0320e+07
I(0) uncertainty (real space) i0_real_error9.9600e+04
Rg (reciprocal space) rg_reciprocal19.58
I(0) (reciprocal space) i0_reciprocal10980000.0000
Solution quality estimate total_estimate0.6799
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.217
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha2.2030
Highest regularization parameter α highest_alpha2293000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.010; Oscil: 0.966; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5p9ua_
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_id5p9uA01
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)