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9v5p

Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207

Method: ELECTRON MICROSCOPY D_max: 106.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v5p
deposition_date	2025-05-26
title	Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207
keywords	DNA methyltransferas 1, inhibitor, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	32.47 Å
rg_electron	31.86 Å
i0	319216000.00
molecular_weight	93190.0 kDa
excluded_volume	88707 Å³
envelope_volume	163210 Å³
shell_volume	42811 Å³
envelope_diameter	113.1 Å
shell_rg	38.53 Å
envelope_rg	31.94 Å
shape_rg	31.84 Å
total_rg	32.30 Å
total_atoms	7004
n_residues	851
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	106.7 Å
rg_real	32.41 Å
rg_real_error	0.73 Å
i0_real	3.1920e+08
i0_real_error	4.8010e+06
rg_reciprocal	32.44 Å
i0_reciprocal	319200000.0000
total_estimate	0.6873
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	39.2 Å
skewness	0.274
kurtosis	-0.418
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	38240000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.998; Smooth: 0.948

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA (cytosine-5)-methyltransferase 1
formula_weight	103882.1 kDa
ec_number	2.1.1.37
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7015

EADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKARESASAKIKEEEAAKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	;DNA (5'-D(CPCPTPTPCPCPGPTPAPAPGPT)-3') ;
formula_weight	3613.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

CCTTCCGTAAGT

Entity 3 polymer

description	;DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') ;
formula_weight	3725.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

ACTTACGGAAGG

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	;(2~{R})-2-[3,5-dicyano-1-[2-[2-(dimethylamino)ethyl-methyl-amino]-2-oxidanylidene-ethyl]-4-ethyl-pyrrolo[2,3-b]pyridin-6-yl]sulfanyl-2-(4-methoxyphenyl)ethanamide ;
formula_weight	533.6 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.85 Å
resolution_method	—
num_particles	338318

fit	/app/data/saxs_computation/v5/9v5p/9v5p.fit
pddf	/app/data/pr_computation/v5/9v5p/9v5p.pr.out
profile	/app/data/saxs_computation/v5/9v5p/9v5p.dat

Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)