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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "DNMT"

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Homo sapiens (19)
	Mus musculus (11)
	synthetic construct (3)

Taxonomy

	Eukaryota (30)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (28)
	ELECTRON MICROSCOPY (1)
	SOLUTION NMR (1)

Polymer Entity Type

	Protein (30)
	DNA (14)

Refinement Resolution (Å)

	1.5 - 2.0 (3)
	2.0 - 2.5 (8)
	2.5 - 3.0 (9)
	3.0 - 3.5 (8)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (8)
	2015 - 2019 (9)
	2020 - 2024 (11)
	2025 - 2029 (1)

Enzyme Classification Name

	Transferases (30)
	Hydrolases (3)

Symmetry Type

	Asymmetric (27)
	Cyclic (3)

SCOP Classification

	All beta proteins (5)
	Alpha and beta proteins (a/b) (5)
	Alpha and beta proteins (a+b) (2)
	Artifacts (2)
	Peptides (2)
	Small proteins (2)

AllSelected

1 to 25 of 30 Structures

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3AV4 \| pdb_00003av4	Download File View File

Crystal structure of mouse DNA methyltransferase 1

Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A., Tajima, S.

(2011) Proc Natl Acad Sci U S A 108: 9055-9059

Released	2011-05-04
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	ZN

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3AV5 \| pdb_00003av5	Download File View File

Crystal structure of mouse DNA methyltransferase 1 with AdoHcy

Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A., Tajima, S.

(2011) Proc Natl Acad Sci U S A 108: 9055-9059

Released	2011-05-04
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAH, ZN

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3AV6 \| pdb_00003av6	Download File View File

Crystal structure of mouse DNA methyltransferase 1 with AdoMet

Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A., Tajima, S.

(2011) Proc Natl Acad Sci U S A 108: 9055-9059

Released	2011-05-04
Method	X-RAY DIFFRACTION 3.09 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAM, ZN

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3EPZ \| pdb_00003epz	Download File View File

Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1

Walker, J.R., Avvakumov, G.V., Xue, S., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2011) J Biological Chem 286: 15344-15351

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	BGC, GOL, NA, ZN

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3PT6 \| pdb_00003pt6	Download File View File

Crystal structure of mouse DNMT1(650-1602) in complex with DNA

Song, J., Patel, D.J.

(2011) Science 331: 1036-1040

Released	2010-12-29
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(CPCPTPGPCPGPGPAPGPGPCPTPCPAPCPGPGPGPA)-3') (nucleic acid) DNA (5'-D(TPCPCPCPGPTPGPAPGPCPCPTPCPCPGPCPAPGPG)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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3PT9 \| pdb_00003pt9	Download File View File

Crystal structure of mouse DNMT1(731-1602) in the free state

Song, J., Patel, D.J.

(2011) Science 331: 1036-1040

Released	2010-12-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAH, ZN

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3PTA \| pdb_00003pta	Download File View File

Crystal structure of human DNMT1(646-1600) in complex with DNA

Song, J., Patel, D.J.

(2011) Science 331: 1036-1040

Released	2010-12-29
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(CPCPTPGPCPGPGPAPGPGPCPTPCPAPCPGPGPGPA)-3') (nucleic acid) DNA (5'-D(TPCPCPCPGPTPGPAPGPCPCPTPCPCPGPCPAPGPG)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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3SWR \| pdb_00003swr	Download File View File

Structure of human DNMT1 (601-1600) in complex with Sinefungin

Hashimoto, H., Cheng, X.

To be published

Released	2011-08-10
Method	X-RAY DIFFRACTION 2.49 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	EDO, MES, SFG, SO4, ZN

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4DA4 \| pdb_00004da4	Download File View File

Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA

Song, J., Patel, D.J.

(2012) Science 335: 709-712

Released	2012-02-22
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA_LOWER_STRAND (nucleic acid) DNA_UPPER_STRAND (nucleic acid)
Unique Ligands	CIT, SAH, ZN

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4WXX \| pdb_00004wxx	Download File View File

The crystal structure of human DNMT1(351-1600)

Zhang, Z.M., Song, J.

(2015) J Mol Biology 427: 2520-2531

Released	2015-07-15
Method	X-RAY DIFFRACTION 2.622 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAH, ZN

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4YOC \| pdb_00004yoc	Download File View File

Crystal Structure of human DNMT1 and USP7/HAUSP complex

Cheng, J., Yang, H., Fang, J., Gong, R., Wang, P., Li, Z., Xu, Y.

(2015) Nat Commun 6: 7023-7023

Released	2015-05-27
Method	X-RAY DIFFRACTION 2.916 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)
Unique Ligands	ZN

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4Z96 \| pdb_00004z96	Download File View File

Crystal structure of DNMT1 in complex with USP7

Zhang, Z.M., Song, J.

To be published

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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4Z97 \| pdb_00004z97	Download File View File

Crystal structure of USP7 in complex with DNMT1(K1115Q)

Zhang, Z.M., Song, J.

To be published

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.998 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)
Unique Ligands	GOL

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5GUT \| pdb_00005gut	Download File View File

The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A

Chen, S.J., Ye, F.

(2018) ACS Chem Biol 13: 772-781

Released	2017-09-06
Method	X-RAY DIFFRACTION 2.099 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	SAH, SO4, ZN

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5GUV \| pdb_00005guv	Download File View File

The crystal structure of mouse DNMT1 (731-1602) mutant - R1279D

Ye, F., Chen, S.J.

(2018) ACS Chem Biol 13: 772-781

Released	2017-08-30
Method	X-RAY DIFFRACTION 3.078 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	ZN

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5WVO \| pdb_00005wvo	Download File View File

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3

Ishiyama, S., Nishiyama, A., Nakanishi, M., Arita, K.

(2017) Mol Cell 68: 350-360.e7

Released	2017-11-15
Method	X-RAY DIFFRACTION 1.997 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Histone H3.1 (protein) Ubiquitin (protein)
Unique Ligands	ZN

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5WY1 \| pdb_00005wy1	Download File View File

Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant)

Kanada, K., Takeshita, K., Suetake, I., Tajima, S., Nakagawa, A.

(2017) J Biochem 162: 271-278

Released	2017-05-24
Method	X-RAY DIFFRACTION 3.27 Å
Organisms	Mus musculus
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein)
Unique Ligands	ZN

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5YDR \| pdb_00005ydr	Download File View File

Structure of DNMT1 RFTS domain in complex with ubiquitin

Qian, C.

(2018) Nucleic Acids Res 46: 3218-3231

Released	2018-02-21
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) Polyubiquitin-B (protein)
Unique Ligands	PO4, ZN

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6W8V \| pdb_00006w8v	Download File View File

Crystal structure of mouse DNMT1 in complex with ACG DNA

Anteneh, H., Song, J.

(2020) Nat Commun

Released	2020-07-08
Method	X-RAY DIFFRACTION 3.12 Å
Organisms	Mus musculus synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) ACG DNA (5'-D(APCPTPTPAP(C49)PGPGPAPAPGPG)-3') (nucleic acid) ACG DNA (5'-D(CPCPTPTPCP(5CM)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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6W8W \| pdb_00006w8w	Download File View File

Crystal structure of mouse DNMT1 in complex with CCG DNA

Anteneh, H., Song, J.

(2020) Nat Commun

Released	2020-07-08
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mus musculus synthetic construct
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) CCG DNA (5'-D(APCPTPTPAP(5CM)PGPGPAPAPGPG)-3') (nucleic acid) CCG DNA (5'-D(CPCPTPTPCP(C49)PGPTPAPAPGPT)-3') (nucleic acid)
Unique Ligands	SAH, ZN

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6X9I \| pdb_00006x9i	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, GOL, SAH, ZN

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6X9J \| pdb_00006x9j	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, X52, ZN

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6X9K \| pdb_00006x9k	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A

Pathuri, S., Horton, J.R., Cheng, X.

(2021) Nat Cancer 2: 1002-1017

Released	2021-07-07
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (5'-D(GPAPGPGPCP(5CM)PGPCPCPTPGPC)-3') (nucleic acid) DNA (5'-D(GPCPAPGPG)-R(P(PYO))-D(PGPGPCPCPTPC)-3') (nucleic acid)
Unique Ligands	EDO, UXM, ZN

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7SFC \| pdb_00007sfc	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	EDO, GOL, I67, ZN

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7SFD \| pdb_00007sfd	Download File View File

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A

Horton, J.R., Pathuri, S., Cheng, X.

(2022) Structure 30: 793-802.e5

Released	2022-03-30
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Homo sapiens
Macromolecule	DNA (cytosine-5)-methyltransferase 1 (protein) DNA (12-MER) (nucleic acid)
Unique Ligands	EDO, GOL, IO5, SAH, ZN

1 to 25 of 30 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3AV4 | pdb_00003av4

3AV5 | pdb_00003av5

3AV6 | pdb_00003av6

3EPZ | pdb_00003epz

3PT6 | pdb_00003pt6

3PT9 | pdb_00003pt9

3PTA | pdb_00003pta

3SWR | pdb_00003swr

4DA4 | pdb_00004da4

4WXX | pdb_00004wxx

4YOC | pdb_00004yoc

4Z96 | pdb_00004z96

4Z97 | pdb_00004z97

5GUT | pdb_00005gut

5GUV | pdb_00005guv

5WVO | pdb_00005wvo

5WY1 | pdb_00005wy1

5YDR | pdb_00005ydr

6W8V | pdb_00006w8v

6W8W | pdb_00006w8w

6X9I | pdb_00006x9i

6X9J | pdb_00006x9j

6X9K | pdb_00006x9k

7SFC | pdb_00007sfc

7SFD | pdb_00007sfd