SAXSdb — 5nrv

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

DNA (cytosine-5)-methyltransferase 3B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	6-dipropylamino-1-hexanol × 2 SULFATE ION × 10 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNM3B_HUMAN
Isoform	Q9UBC3-6
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 218–367 Author chain D； PDBConstruct 1–150； UniProt 218–367

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	5nrv
Deposition date deposition_date	2017-04-25
Structure title title	Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol
Keywords keywords	DNMT3B PWWP DOMAIN, HISTONE BINDING, BETA BARREL, LIGAND, 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.

5nrv__assembly_1__model_1

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

Download this curve (.dat)

5nrv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5nrv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.58 Å
Rg (electron density)	20.87 Å
Total Rg	21.71 Å
Atom count	2165
Residues	260
Excluded volume	38709 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5nrv__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	DNA (cytosine-5)-methyltransferase 3B
Molecular weight formula_weight	16698.8 kDa
EC 编号 ec_number	2.1.1.37
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A
Atom count atom_count	2348

EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	6-dipropylamino-1-hexanol
Molecular weight formula_weight	201.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5nrva_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.2 — PWWP domain

Domain ID domain_id	d5nrvd_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.2 — PWWP domain

CATH v4.4 (4 domains)

Domain ID domain_id	5nrvA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	5nrvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	50 — PWWP, helical domain

Domain ID domain_id	5nrvD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	5nrvD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	50 — PWWP, helical domain

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Unit-cell length a length_a	73.550 Å
Unit-cell length b length_b	73.550 Å
Unit-cell length c length_c	155.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.075 Å
Low-resolution limit resolution_low	40.173 Å
R factor r_factor	0.2089
R_work r_work	0.2071
R_free r_free	0.2435

Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol

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

DNA (cytosine-5)-methyltransferase 3B

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

5nrv__assembly_1__model_1

5nrv__assembly_1__model_1 | I(q)

5nrv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol

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

DNA (cytosine-5)-methyltransferase 3B

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

5nrv__assembly_1__model_1

5nrv__assembly_1__model_1 | I(q)

5nrv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)