SAXSdb — 5lr6

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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	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone × 1 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 CHLORIDE 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	—
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 Author chain C； PDBConstruct 1–221； UniProt 44–264 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5lr6
Deposition date deposition_date	2016-08-18
Structure title title	Crystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-yl)methanone
Keywords keywords	METHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, 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.

5lr6__assembly_1__model_1

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

Download this curve (.dat)

5lr6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5lr6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.70 Å
Rg (electron density)	16.48 Å
Total Rg	17.49 Å
Atom count	1694
Residues	212
Excluded volume	30449 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5lr6__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5lr6__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5lr6__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5lr6__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 (5)

Entity 1 Entity 1 polymer

Description description	Catechol O-methyltransferase
Molecular weight formula_weight	24694.3 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	7062

MGDTKEQRILRYVQQNAKPGDPQSVLEAIDTYCTQKEWAMNVGDAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEINPDCAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEKCGLLRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSSYLEYMKVVDGLEKAIYQGPSSPDKS

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1~{H}-pyrazol-3-yl]-(4-phenylpiperazin-1-yl)methanone
Molecular weight formula_weight	367.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 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	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	243

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5lr6a_
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	d5lr6b_
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	d5lr6c_
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	d5lr6d_
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	5lr6A00
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	5lr6B00
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	5lr6C00
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	5lr6D00
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	70.983 Å
Unit-cell length b length_b	103.621 Å
Unit-cell length c length_c	78.409 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
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	2.300 Å
Low-resolution limit resolution_low	46.938 Å
R factor r_factor	0.2035
R_work r_work	0.1957
R_free r_free	0.2227

Crystal Structure of COMT in complex with [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-yl)methanone

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

5lr6__assembly_1__model_1

5lr6__assembly_1__model_1 | I(q)

5lr6__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 (5)

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 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 [3-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-5-yl]-(4-phenylpiperazin-1-yl)methanone

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

5lr6__assembly_1__model_1

5lr6__assembly_1__model_1 | I(q)

5lr6__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)