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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Desoky, A.Y."

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Search Summary

This query matches 12 Structures.

Refinements

Structure Determination Methodology

experimental (12)

Scientific Name of Source Organism

	Homo sapiens (9)
	Mus musculus (4)
	synthetic construct (3)
	Xenopus laevis (2)

Taxonomy

	Eukaryota (12)
	other sequences (3)

Experimental Method

	X-RAY DIFFRACTION (9)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

	Protein (12)
	DNA (6)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (4)
	2.5 - 3.0 (1)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	2015 - 2019 (2)
	2020 - 2024 (10)

Enzyme Classification Name

	Transferases (9)
	Hydrolases (2)
	Lyases (2)

Symmetry Type

	Asymmetric (11)
	Cyclic (1)

SCOP Classification

	All beta proteins (2)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 12 of 12 Structures

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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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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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8VX4 \| pdb_00008vx4	Download File View File

Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle

You, Q., Li, H.

(2024) Commun Biol 7: 1202-1202

Released	2024-10-09
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	N-glycosylase/DNA lyase (protein) DNA (35-MER) (nucleic acid)

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8VX5 \| pdb_00008vx5	Download File View File

Nucleosome core particle containing an 8-oxoG damage site

You, Q., Li, H.

(2024) Commun Biol 7: 1202-1202

Released	2024-10-09
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2

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8VX6 \| pdb_00008vx6	Download File View File

Human OGG1 bound at the nucleosomal DNA entry site

You, Q., Li, H.

(2024) Commun Biol 7: 1202-1202

Released	2024-10-09
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Homo sapiens Xenopus laevis synthetic construct
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 2

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8XV4 \| pdb_00008xv4	Download File View File

Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

Du, X., Gan, Q., Xu, J., Liu, J.

(2025) Nat Commun 16: 474-474

Released	2024-11-06
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Developmental pluripotency-associated protein 3 (protein) E3 ubiquitin-protein ligase UHRF1 (protein)
Unique Ligands	ZN

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8XV6 \| pdb_00008xv6	Download File View File

Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

Du, X., Gan, Q., Xu, J., Liu, J.

(2025) Nat Commun 16: 474-474

Released	2024-11-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Developmental pluripotency-associated protein 3 (protein) E3 ubiquitin-protein ligase UHRF1 (protein)
Unique Ligands	GOL, SCN, ZN

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8XV7 \| pdb_00008xv7	Download File View File

Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)

Du, X., Gan, Q., Xu, J., Liu, J.

(2025) Nat Commun 16: 474-474

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	Developmental pluripotency-associated protein 3 (protein) E3 ubiquitin-protein ligase UHRF1 (protein)
Unique Ligands	ACY, GOL, ZN

Explore in 3D

8XV8 \| pdb_00008xv8	Download File View File

Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)

Du, X., Gan, Q., Xu, J., Liu, J.

(2025) Nat Commun 16: 474-474

Released	2024-11-06
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	Developmental pluripotency-associated protein 3 (protein) E3 ubiquitin-protein ligase UHRF1 (protein)
Unique Ligands	ZN

1 to 12 of 12 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

5GUT | pdb_00005gut

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

5GUV | pdb_00005guv

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

6X9I | pdb_00006x9i

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

6X9J | pdb_00006x9j

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

6X9K | pdb_00006x9k

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

8VX4 | pdb_00008vx4

Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle

8VX5 | pdb_00008vx5

Nucleosome core particle containing an 8-oxoG damage site

8VX6 | pdb_00008vx6

Human OGG1 bound at the nucleosomal DNA entry site

8XV4 | pdb_00008xv4

Crystal structure of TTD-PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

8XV6 | pdb_00008xv6

Crystal structure of PHD domain of UHRF1 in complex with mStella peptide (residues 85-119)

8XV7 | pdb_00008xv7

Crystal structure of TTD-PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)

8XV8 | pdb_00008xv8

Crystal structure of PHD domain of UHRF1 in complex with hStella peptide (residues 75-121)

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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

5GUT | pdb_00005gut

5GUV | pdb_00005guv

6X9I | pdb_00006x9i

6X9J | pdb_00006x9j

6X9K | pdb_00006x9k

8VX4 | pdb_00008vx4

8VX5 | pdb_00008vx5

8VX6 | pdb_00008vx6

8XV4 | pdb_00008xv4

8XV6 | pdb_00008xv6

8XV7 | pdb_00008xv7

8XV8 | pdb_00008xv8