SAXSdb — 5k0n

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Catechol O-methyltransferase

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 MAGNESIUM ION × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole × 1 POTASSIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole × 1 POTASSIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2 5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole × 1 POTASSIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 MAGNESIUM ION × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 2 5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole × 1 POTASSIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COMT_RAT
Isoform	P22734-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 2–221 Author chain B； PDBConstruct 1–220； UniProt 2–221 Author chain C； PDBConstruct 1–220； UniProt 2–221 Author chain D； PDBConstruct 1–220； UniProt 2–221

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5k0n
Deposition date deposition_date	2016-05-17
Structure title title	Crystal Structure of COMT in complex with 4-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-3-yl]-1,3-dimethylpyrazole
Keywords keywords	METHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, CATECHOL, transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5k0n__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5k0n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k0n__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.24 Å
Rg (electron density)	17.11 Å
Total Rg	18.07 Å
Atom count	1761
Residues	220
Excluded volume	31668 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k0n__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5k0n__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5k0n__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5k0n__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Catechol O-methyltransferase
Molecular weight formula_weight	24563.1 kDa
EC 编号 ec_number	2.1.1.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7717

GDTKEQRILRYVQQNAKPGDPQSVLEAIDTYCTQKEWAMNVGDAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEINPDCAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEKCGLLRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSSYLEYMKVVDGLEKAIYQGPSSPDKS

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
Molecular weight formula_weight	207.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	5-[1-(4-methoxyphenyl)cyclopropyl]-1',3'-dimethyl-1'H,2H-3,4'-bipyrazole
Molecular weight formula_weight	308.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	617

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5k0na_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.1 — COMT-like

Domain ID domain_id	d5k0nb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.1 — COMT-like

Domain ID domain_id	d5k0nc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.1 — COMT-like

Domain ID domain_id	d5k0nd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.1 — COMT-like

CATH v4.4 (4 domains)

Domain ID domain_id	5k0nA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5k0nB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5k0nC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	5k0nD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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Unit-cell length a length_a	77.023 Å
Unit-cell length b length_b	69.890 Å
Unit-cell length c length_c	104.102 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	45.418 Å
R factor r_factor	0.1862
R_work r_work	0.1838
R_free r_free	0.2325

Crystal Structure of COMT in complex with 4-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-3-yl]-1,3-dimethylpyrazole

1. Protein Identity and Related Structures Protein Identity & Related Structures

Catechol O-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5k0n__assembly_1__model_1

5k0n__assembly_1__model_1 | I(q)

5k0n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of COMT in complex with 4-[5-[1-(4-methoxyphenyl)cyclopropyl]-1H-pyrazol-3-yl]-1,3-dimethylpyrazole

1. Protein Identity and Related Structures Protein Identity & Related Structures

Catechol O-methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5k0n__assembly_1__model_1

5k0n__assembly_1__model_1 | I(q)

5k0n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)