1m0e

ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE

Method: X-RAY DIFFRACTION D_max: 86.0 Å Quality: REASONABLE

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

Modification methylase HhaI

Haemophilus haemolyticus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–327	Not recorded	5'-D(PCPCPAPTPGPCPGPCPTPGPAPC)-3' × 1 5'-D(PGPTPCPAPGP(Z)PGPCPAPTPGPG)-3' × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 8000, Ca acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.243

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1M0E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10MH TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET Deposited 1998-08-10	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；10% (W/V) PEG 8000 50 MM CALCIUM ACETATE 50 MM SODIUM CACODYLATE PH 6.5	Resolution 2.55 Å
1FJX STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY Deposited 2000-08-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：T250G	SO4 SULFATE ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；2.7 M ammonium sulfate 20% (w/v) glucose 50 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 16K	Resolution 2.26 Å R-free 0.283
1HMY CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE Deposited 1993-08-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–327（327 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1MHT COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE Deposited 1994-12-08	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；289 K；BIS-TRIS-PROPANE_HCL, NACL, EDTA, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K	Resolution 2.60 Å
1SKM HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site Deposited 2004-03-05	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.20 Å R-free 0.221
1SVU Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions Deposited 2004-03-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–327（327 aa）	Mutation：Q237W	SO4 SULFATE ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289 K；ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.66 Å R-free 0.266
1SVU Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions Deposited 2004-03-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–327（327 aa）	Mutation：Q237W	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；289 K；ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.66 Å R-free 0.266
2C7O HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5 % GLUCOSE.	Resolution 1.90 Å R-free 0.215
2C7P HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH Deposited 2005-11-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 5 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.4 M AMMONIUM SULFATE	Resolution 1.70 Å R-free 0.220
2C7Q HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH Deposited 2005-11-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 3 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE	Resolution 1.85 Å R-free 0.210
2C7R HhaI DNA methyltransferase (T250G mutant) complex with oligonucleotide containing 2-aminopurine as a target base (GPGC:GMGC) and SAH Deposited 2005-11-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：YES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 7 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.7 M AMMONIUM SULFATE, 5 % GLUCOSE	Resolution 1.90 Å R-free 0.217
2HMY BINARY COMPLEX OF HHAI METHYLTRANSFERASE WITH ADOMET FORMED IN THE PRESENCE OF A SHORT NONPSECIFIC DNA OLIGONUCLEOTIDE Deposited 1999-02-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–327（327 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；2.2M AMMONIUM SULFATE 50 MMSODIUM CITRATE PH 6.0	Resolution 2.61 Å
2HR1 Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy Deposited 2006-07-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；Ammonium Sulfate 15%, Sodium Citrate 100 mM, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.96 Å R-free 0.269
2I9K Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI Deposited 2006-09-05	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：F124A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；290 K；20% Ammonium Sulfate, 100mM Sodium Citrate buffer, pH 6.0, hanging drop, temperature 290K	Resolution 2.65 Å R-free 0.262
2UYC HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH Deposited 2007-04-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：YES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 6 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE, 5% GLUCOSE	Resolution 2.00 Å R-free 0.227
2UYH HhaI DNA methyltransferase S87Q-Q237S mutant complex with 13mer GCGC- GMGC oligonucleotide and SAH Deposited 2007-04-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：YES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.6 M AMMONIUM SULFATE, 5% GLUCOSE	Resolution 2.63 Å R-free 0.258
2UZ4 HhaI DNA methyltransferase R165N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH Deposited 2007-04-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：YES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；50 MM NA CITRATE PH 5.6, 1.8 M AMMONIUM SULFATE	Resolution 2.10 Å R-free 0.235
2Z6A S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation Deposited 2007-07-25	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：C81A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；2.0M Ammonium Sulfate, 50mM Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.88 Å R-free 0.280
2Z6Q Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy Deposited 2007-08-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain A 1–327（327 aa）	Mutation：R165A	DCZ 2'-DEOXYCYTIDINE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100 mM sodium citrate (pH 6.0), ammonium sulfate 1.2M, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.79 Å R-free 0.269
2Z6U Ternary structure of the Glu119Ala M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy Deposited 2007-08-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：E119A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100mM sodium citrate buffer, 45%-55% 3.5M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.72 Å R-free 0.267
2ZCJ Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy Deposited 2007-11-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Mutation：E119Q	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；100 mM Sodium Citrate, 1.6-2.1 Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.75 Å R-free 0.266
3EEO M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the deoxycytidine residue targeted for methylation. Deposited 2008-09-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.94 Å R-free 0.275
3MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH UNMODIFIED DNA AND ADOHCY Deposited 1996-07-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
4MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DNA AND ADOHCY Deposited 1996-07-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
5CIY Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain Deposited 2015-07-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；AMMONIUM SULFATE 1.8 M, CITRATE 50mM	Resolution 1.59 Å R-free 0.188
5LOD Crystal structure of HhaI DNA methyltransferase in APO form Deposited 2016-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–327（327 aa） Chain B 1–327（327 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；AMMONIUM SULFATE 50 mM, CITRATE 100mM, 32% (w/v) PEG-4000	Resolution 1.90 Å R-free 0.219
5MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH HEMIMETHYLATED DNA AND ADOHCY Deposited 1996-10-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；10% PEG 8000, 50 MM CA-ACETATE, 50 MM SODIUM CACODYLATE PH 6.5	Resolution 2.70 Å
6MHT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND DNA CONTAINING 4'-THIO-2'DEOXYCYTIDINE AT THE TARGET Deposited 1998-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；293 K；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6, temperature 293.0K	Resolution 2.05 Å R-free 0.231
7MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-05	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6	Resolution 2.87 Å
8MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.4-1.8 M AMMONIUM SULFATE 50 MM CITRATE PH 5.6	Resolution 2.76 Å
9MHT CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX Deposited 1998-08-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–327（327 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；10% (W/V) POLYETHYLENE GLYCOL 8000 50 MM CA-ACETATE 50 MM SODIUM CACODYLATE PH 5.6	Resolution 2.39 Å

30 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTH1_HAEHA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–327； UniProt 1–327

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1m0e
Deposition date deposition_date	2002-06-12
Structure title title	ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE
Keywords keywords	Protein-DNA covalent complex, Mechanism based DNA methylation inhibitors, Zebularine, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.65 Å
Radius of gyration Rg (electron density) rg_electron	20.63 Å
Forward intensity I(0) i0	40557500.00
Molecular weight molecular_weight	44587.0 kDa
Excluded volume excluded_volume	53669 Å³
Envelope volume envelope_volume	62130 Å³
Hydration-shell volume shell_volume	24536 Å³
Envelope diameter envelope_diameter	81.0 Å
Shell Rg shell_rg	27.95 Å
Envelope Rg envelope_rg	21.09 Å
Shape Rg shape_rg	20.61 Å
Total Rg total_rg	21.49 Å
Total atoms total_atoms	3134
Residues n_residues	350
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.0 Å
Rg (real space) rg_real	21.55 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	4.0560e+07
I(0) uncertainty (real space) i0_real_error	6.4240e+05
Rg (reciprocal space) rg_reciprocal	21.57 Å
I(0) (reciprocal space) i0_reciprocal	40560000.0000
Solution quality estimate total_estimate	0.7046
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.289
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	8955000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.448; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	5'-D(PCPCPAPTPGPCPGPCPTPGPAPC)-3'
Molecular weight formula_weight	3623.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	3379

CCATGCGCTGAC

Entity 2 Entity 2 polymer

Description description	5'-D(PGPTPCPAPGP(Z)PGPCPAPTPGPG)-3'
Molecular weight formula_weight	3688.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GTCAGCGCATGG

Entity 3 Entity 3 polymer

Description description	Modification methylase HhaI
Molecular weight formula_weight	37042.2 kDa
EC 编号 ec_number	2.1.1.73
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY

来源 Source

来源生物 organism	Haemophilus haemolyticus
NCBI Class编号 ncbi_taxonomy_id	726
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	245

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1m0ea_
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.66.1.26 — C5 cytosine-specific DNA methylase, DCM

CATH v4.4 (2 domains)

Domain ID domain_id	1m0eA01
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	1m0eA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	120 — DNA Methylase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Methylase, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	96.190 Å
Unit-cell length b length_b	96.190 Å
Unit-cell length c length_c	315.750 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	39.700 Å
R factor r_factor	—
R_work r_work	0.1770
R_free r_free	0.2430

fit	/app/data/saxs_computation/m0/1m0e/1m0e.fit
pddf	/app/data/pr_computation/m0/1m0e/1m0e.pr.out
profile	/app/data/saxs_computation/m0/1m0e/1m0e.dat

ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE

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

Modification methylase HhaI

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)