SAXSdb — 3rc0

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

N-lysine methyltransferase SETD6

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transcription factor p65 peptide × 1 （Q04206） 1,2-ETHANEDIOL × 10 S-ADENOSYLMETHIONINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Transcription factor p65 peptide × 1 （Q04206） 1,2-ETHANEDIOL × 6 S-ADENOSYLMETHIONINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SETD6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–449； UniProt 1–449 Author chain B； PDBConstruct 1–449； UniProt 1–449

Transcription factor p65 peptide

OrganismNot specified

UniProt Q04206

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	N-lysine methyltransferase SETD6 × 1 （Q8TBK2） 1,2-ETHANEDIOL × 10 S-ADENOSYLMETHIONINE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N-lysine methyltransferase SETD6 × 1 （Q8TBK2） 1,2-ETHANEDIOL × 6 S-ADENOSYLMETHIONINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF65_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–15； UniProt 302–316 Author chain Q； PDBConstruct 1–15； UniProt 302–316

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	3rc0
Deposition date deposition_date	2011-03-30
Structure title title	Human SETD6 in complex with RelA Lys310 peptide
Keywords keywords	Epigenetics, protein lysine monomethylation, Mammalian nuclear factor kB (NF-kB), 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.

3rc0__assembly_1__model_1

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

Download this curve (.dat)

3rc0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rc0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.91 Å
Rg (electron density)	24.03 Å
Total Rg	24.91 Å
Atom count	3389
Residues	426
Excluded volume	60607 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rc0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rc0__assembly_2__model_1`	dimeric （2）	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	N-lysine methyltransferase SETD6
Molecular weight formula_weight	50837.8 kDa
EC 编号 ec_number	2.1.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7181

MATQAKRPRVAGPVDGGDLDPVACFLSWCRRVGLELSPKVAVSRQGTVAGYGMVARESVQAGELLFVVPRAALLSQHTCSIGGLLERERVALQSQSGWVPLLLALLHELQAPASRWRPYFALWPELGRLEHPMFWPEEERRCLLQGTGVPEAVEKDLANIRSEYQSIVLPFMEAHPDLFSLRVRSLELYHQLVALVMAYSFQEPLEEEEDEKEPNSPVMVPAADILNHLANHNANLEYSANCLRMVATQPIPKGHEIFNTYGQMANWQLIHMYGFVEPYPDNTDDTADIQMVTVREAALQGTKTEAERHLVYERWDFLCKLEMVGEEGAFVIGREEVLTEEELTTTLKVLCMPAEEFRELKDQDGGGDDKREEGSLTITNIPKLKASWRQLLQNSVLLTLQTYATDLKTDQGLLSNKEVYAKLSWREQQALQVRYGQKMILHQLLELTS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Transcription factor p65 peptide
Molecular weight formula_weight	1909.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

RKRTYETFKSIMKKS

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	485

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3rc0A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	3rc0A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

Domain ID domain_id	3rc0B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1410 — set domain protein methyltransferase, domain 1
Homologous superfamily homologous superfamily	10 — set domain protein methyltransferase, domain 1

Domain ID domain_id	3rc0B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1420 — set domain protein methyltransferase, domain 2
Homologous superfamily homologous superfamily	10 — Rubisco LSMT, substrate-binding domain

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Unit-cell length a length_a	61.621 Å
Unit-cell length b length_b	64.501 Å
Unit-cell length c length_c	73.759 Å
Unit-cell angle α angle_alpha	78.73 °
Unit-cell angle β angle_beta	70.60 °
Unit-cell angle γ angle_gamma	64.21 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	34.720 Å
R factor r_factor	0.1688
R_work r_work	0.1661
R_free r_free	0.2343

Human SETD6 in complex with RelA Lys310 peptide

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

N-lysine methyltransferase SETD6

State in the Current Structure

Other States of the Same Protein in the Database

Transcription factor p65 peptide

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

3rc0__assembly_1__model_1

3rc0__assembly_1__model_1 | I(q)

3rc0__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Human SETD6 in complex with RelA Lys310 peptide

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

N-lysine methyltransferase SETD6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription factor p65 peptide

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

3rc0__assembly_1__model_1

3rc0__assembly_1__model_1 | I(q)

3rc0__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)