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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P26358 New Search
25PDB entries
27Biological assembly
27chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3EPZ Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 Deposited 2008-09-30 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 351–600（250 aa） Fragment：REPLICATION FOCI-TARGETING SEQUENCE
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 BGC beta-D-glucopyranose × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；298 K；23 % PEG 3350, 0.1 M BIS-TRIS PH 6.0,0.2 M SODIUM ACETATE, 0.005 M TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 6.00
Resolution 2.31 Å R-free 0.264
3EPZ Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1 Deposited 2008-09-30 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 351–600（250 aa） Fragment：REPLICATION FOCI-TARGETING SEQUENCE
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；298 K；23 % PEG 3350, 0.1 M BIS-TRIS PH 6.0,0.2 M SODIUM ACETATE, 0.005 M TCEP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 6.00
Resolution 2.31 Å R-free 0.264
3PTA Crystal structure of human DNMT1(646-1600) in complex with DNA Deposited 2010-12-02 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 646–1600（955 aa） Fragment：UNP residues 646-1600
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；6% PEG 20,000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 3.60 Å R-free 0.291
3SWR Structure of human DNMT1 (601-1600) in complex with Sinefungin Deposited 2011-07-14 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 601–1600（1000 aa） Fragment：sequence database residues 601-1600
Not recorded SFG SINEFUNGIN × 1 SO4 SULFATE ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 EDO 1,2-ETHANEDIOL × 25 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；289 K；5% PEG 4000, 5 mM MgSO4, 50 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.49 Å R-free 0.272
4WXX The crystal structure of human DNMT1(351-1600) Deposited 2014-11-14 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 15–1264（1250 aa）
Not recorded ZN ZINC ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；45% PEG200, 50 mM CaCl2, 0.1 mM MES
Resolution 2.62 Å R-free 0.245
4WXX The crystal structure of human DNMT1(351-1600) Deposited 2014-11-14 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 15–1264（1250 aa）
Not recorded ZN ZINC ION × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；45% PEG200, 50 mM CaCl2, 0.1 mM MES
Resolution 2.62 Å R-free 0.245
4YOC Crystal Structure of human DNMT1 and USP7/HAUSP complex Deposited 2015-03-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 600–1600（1001 aa） Fragment：UNP RESIDUES 600-1600
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；6-8% PEG 3350, 200 mM potassium acetate
Resolution 2.92 Å R-free 0.258
4Z96 Crystal structure of DNMT1 in complex with USP7 Deposited 2015-04-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 1097–1129（33 aa） Fragment：UNP residues 1097-1129
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH5.5, 10% PEG6000, 15% glycerol
Resolution 2.85 Å R-free 0.246
5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 351–600（250 aa） Fragment：RFTS domain, UNP residues 351-600
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000
Resolution 2.00 Å R-free 0.239
5YDR Structure of DNMT1 RFTS domain in complex with ubiquitin Deposited 2017-09-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 351–599（249 aa） Fragment：RFTS domain, UNP residues 351-599
Not recorded PO4 PHOSPHATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000
Resolution 2.00 Å R-free 0.233
6L1F Crystal structure of PHF20L1 Tudor1 in complex with K142me1 DNMT1 Deposited 2019-09-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 140–145（6 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；30% PEG MME 2000, 0.1M sodium cacodylate, pH 6.0
Resolution 1.90 Å R-free 0.230
6X9I Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA Deposited 2020-06-02 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.20 Å R-free 0.225
6X9J Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052 Deposited 2020-06-02 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 X52 N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 1.79 Å R-free 0.229
6X9K Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A Deposited 2020-06-02 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 9 UXM (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.65 Å R-free 0.228
7SFC Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A Deposited 2021-10-03 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded ZN ZINC ION × 2 I67 N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide × 3 EDO 1,2-ETHANEDIOL × 19 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 1.97 Å R-free 0.208
7SFD Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A Deposited 2021-10-03 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 IO5 (2S)-2-({3,5-dicyano-4-ethyl-6-[4-(2-hydroxyethyl)-1,4-diazepan-1-yl]pyridin-2-yl}sulfanyl)-2-phenylacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.09 Å R-free 0.216
7SFE Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830334A Deposited 2021-10-03 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 ZN ZINC ION × 2 GOL GLYCEROL × 1 96I (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]amino}-2-phenylacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.55 Å R-free 0.236
7SFF Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B Deposited 2021-10-03 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 1 C79 (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.05 Å R-free 0.217
7SFG Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Cofactor SAM Deposited 2021-10-03 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 393–1264（872 aa）
Not recorded ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；292 K；14-18% polyethylene glycol (PEG) 3350, 0.1 M citric acid (pH 5.1)
Resolution 2.43 Å R-free 0.223
7XI9 Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form) Deposited 2022-04-12 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 351–1616（1266 aa）
Not recorded ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging
Resolution 2.52 Å
7XIB Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form) Deposited 2022-04-12 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 351–1616（1266 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging
Resolution 2.23 Å
8V9U Solution NMR structure of human DNMT1 N-terminal alpha-helical domain Deposited 2023-12-09 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 16–93（78 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 1 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-13C; U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-15N] DNMT1, 20 mM MES/Bis-Tris, 50 mM sodium chloride, 5 % pentaethylene glycol monododecyl ether (C12E5), 95 % n-hexanol, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8XQC Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog Deposited 2024-01-05 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 351–1616（1266 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9K2W Cryo-EM structure of USP7:DNMT1 complex; closed conformation Deposited 2024-10-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 351–1616（1266 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9K2X Cryo-EM structure of USP7:DNMT1 complex; open conformation Deposited 2024-10-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 351–1616（1266 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9V36 Human DNMT1 (aa 698-1616) bound to hemimethylated dsDNA and Inhibitor DMI26 Deposited 2025-05-21 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 698–1616（919 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 A1EQT (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-phenyl-ethanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
9V5P Human DNMT1 (aa 698-1616) in complex with hemimethylated dsDNA and inhibitor DMT207 Deposited 2025-05-26 Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric（3） Consistent with all polymers
Chain A 698–1616（919 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 A1EQ2 (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 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.