RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

235,458 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Gene Name = "BPSL2098"

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 60 Structures.

Refinements

Structure Determination Methodology

experimental (60)

Scientific Name of Source Organism

	Homo sapiens (60)
	synthetic construct (2)
	Urechis caupo (1)

Taxonomy

	Eukaryota (60)
	Eukaryota (eukaryotes) (6)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (60)

Polymer Entity Type

Protein (60)

Refinement Resolution (Å)

	1.5 - 2.0 (11)
	2.0 - 2.5 (40)
	2.5 - 3.0 (9)

Release Date

	2005 - 2009 (14)
	2010 - 2014 (3)
	2015 - 2019 (37)
	2020 - 2024 (6)

Enzyme Classification Name

Oxidoreductases (60)

Symmetry Type

	Asymmetric (59)
	Cyclic (1)

SCOP Classification

	All beta proteins (42)
	Artifacts (2)

AllSelected

1 to 25 of 60 Structures

Page 1 of 3

Sort by

Explore in 3D

2GF7 \| pdb_00002gf7	Download File View File

Double tudor domain structure

Huang, Y., Fang, J., Bedford, M.T., Zhang, Y., Xu, R.M.

(2006) Science 312: 748-751

Released	2006-05-02
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Jumonji domain-containing protein 2A (protein)
Unique Ligands	SO4

Explore in 3D

2GFA \| pdb_00002gfa	Download File View File

double tudor domain complex structure

Huang, Y., Fang, J., Bedford, M.T., Zhang, Y., Xu, R.M.

(2006) Science 312: 748-751

Released	2006-05-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Jumonji domain-containing protein 2A (protein) peptide (protein)

Explore in 3D

2OQ6 \| pdb_00002oq6	Download File View File

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9

Pilka, E.S., Ng, S.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

(2007) Nature 448: 87-91

Released	2007-03-13
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) synthetic peptide (protein)
Unique Ligands	NI, OGA, ZN

Explore in 3D

2OQ7 \| pdb_00002oq7	Download File View File

The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine

Kavanagh, K.L., Ng, S.S., Pilka, E., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

(2007) Nature 448: 87-91

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein)
Unique Ligands	NI, OGA, ZN

Explore in 3D

2OS2 \| pdb_00002os2	Download File View File

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36

(2007) Nature 448: 87-91

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) histone 3 peptide (protein)
Unique Ligands	NI, OGA, ZN

Explore in 3D

2OT7 \| pdb_00002ot7	Download File View File

Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9

(2007) Nature 448: 87-91

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.135 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) histone 3 K9 monomethyl (protein)
Unique Ligands	NI, OGA, ZN

Explore in 3D

2OX0 \| pdb_00002ox0	Download File View File

Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9

(2007) Nature 448: 87-91

Released	2007-03-13
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) synthetic peptide (protein)
Unique Ligands	CL, NI, OGA, ZN

Explore in 3D

2P5B \| pdb_00002p5b	Download File View File

The complex structure of JMJD2A and trimethylated H3K36 peptide

Zhang, G., Chen, Z., Zang, J., Hong, X., Shi, Y.

(2007) Proc Natl Acad Sci U S A 104: 10818-10823

Released	2007-06-12
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens Urechis caupo
Macromolecule	Histone H3 (protein) JmjC domain-containing histone demethylation protein 3A (protein)
Unique Ligands	FE2, OGA, OXY, ZN

Explore in 3D

2PXJ \| pdb_00002pxj	Download File View File

The complex structure of JMJD2A and monomethylated H3K36 peptide

Chen, Z., Zang, J., Kappler, J., Hong, X., Crawford, F., Zhang, G.

(2007) Proc Natl Acad Sci U S A 104: 10818-10823

Released	2007-06-12
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) monomethylated Histone H3K36 peptide (protein)
Unique Ligands	FE2, OGA, ZN

Explore in 3D

2Q8C \| pdb_00002q8c	Download File View File

Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate

Couture, J.-F., Collazo, E., Ortiz-Tello, P., Brunzelle, J.S., Trievel, R.C.

(2007) Nat Struct Mol Biol 14: 689-695

Released	2007-07-03
Method	X-RAY DIFFRACTION 2.047 Å
Organisms	Homo sapiens
Macromolecule	HISTONE 3 PEPTIDE (protein) JmjC domain-containing histone demethylation protein 3A (protein)
Unique Ligands	AKG, NI, ZN

Explore in 3D

2Q8D \| pdb_00002q8d	Download File View File

Crystal structure of JMJ2D2A in ternary complex with histone H3-K36me2 and succinate

Couture, J.-F., Collazo, E., Ortiz-Tello, P., Brunzelle, J.S., Trievel, R.C.

(2007) Nat Struct Mol Biol 14: 689-695

Released	2007-07-03
Method	X-RAY DIFFRACTION 2.29 Å
Organisms	Homo sapiens
Macromolecule	HISTONE 3 peptide (protein) JmjC domain-containing histone demethylation protein 3A (protein)
Unique Ligands	NI, SIN, ZN

Explore in 3D

2Q8E \| pdb_00002q8e	Download File View File

Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase

Couture, J.-F., Collazo, E., Ortiz-Tello, P., Brunzelle, J.S., Trievel, R.C.

(2007) Nat Struct Mol Biol 14: 689-695

Released	2007-07-03
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) histone 3 peptide (protein)
Unique Ligands	NI, OGA, ZN

Explore in 3D

2QQR \| pdb_00002qqr	Download File View File

JMJD2A hybrid tudor domains

Lee, J., Botuyan, M.V., Mer, G.

(2008) Nat Struct Mol Biol 15: 109-111

Released	2007-12-11
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein)
Unique Ligands	SO4

Explore in 3D

2QQS \| pdb_00002qqs	Download File View File

JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide

Lee, J., Botuyan, M.V., Mer, G.

(2008) Nat Struct Mol Biol 15: 109-111

Released	2007-12-11
Method	X-RAY DIFFRACTION 2.82 Å
Organisms	Homo sapiens
Macromolecule	JmjC domain-containing histone demethylation protein 3A (protein) METHYLATED HISTONE H4 PEPTIDE (protein)

Explore in 3D

3RVH \| pdb_00003rvh	Download File View File

Crystal Structure of JMJD2A Complexed with Inhibitor

King, O.N.F., Maloney, D.J., Tumber, A., Rai, G., Jadhav, A., Clifton, I.J., Heightman, T.D., Simeonov, A., McDonough, M.A., Schofield, C.J.

To be published

Released	2012-05-09
Method	X-RAY DIFFRACTION 2.251 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	GOL, HQ2, NI, ZN

Explore in 3D

3U4S \| pdb_00003u4s	Download File View File

Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine

Ma, J., McDonough, M.A., Schofield, C.J.

(2012) Angew Chem Int Ed Engl 51: 1631-1634

Released	2012-02-08
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	HISTONE 3 TAIL ANALOG (T11C Peptide) (protein) Lysine-specific demethylase 4A (protein)
Unique Ligands	08P, NI, ZN

Explore in 3D

4GD4 \| pdb_00004gd4	Download File View File

Crystal Structure of JMJD2A Complexed with Inhibitor

King, O.N.F., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., McDonough, M.A., Schofield, C.J., Structural Genomics Consortium (SGC)

To be published

Released	2012-08-15
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	0WS, CL, NI, ZN

Explore in 3D

5D6W \| pdb_00005d6w	Download File View File

Crystal structure of double tudor domain of human lysine demethylase KDM4A

Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

(2016) Nat Commun 7: 13387-13387

Released	2015-11-25
Method	X-RAY DIFFRACTION 1.992 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	SRT

Explore in 3D

5D6X \| pdb_00005d6x	Download File View File

Crystal structure of double tudor domain of human lysine demethylase KDM4A

Wang, F., Su, Z., Denu, J.M., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

(2016) Nat Commun 7: 13387-13387

Released	2015-11-25
Method	X-RAY DIFFRACTION 2.153 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	SO4

Explore in 3D

5D6Y \| pdb_00005d6y	Download File View File

Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3

Wang, F., Su, Z., Miller, M.D., Denu, J.M., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

(2016) Nat Commun 7: 13387-13387

Released	2016-02-10
Method	X-RAY DIFFRACTION 2.287 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein) peptide H3K23me3 (19-28) (protein)

Explore in 3D

5F2S \| pdb_00005f2s	Download File View File

Crystal structure of human KDM4A in complex with compound 15

Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.

(2016) J Med Chem 59: 1388-1409

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	5TZ, CL, DMS, EDO, ZN

Explore in 3D

5F2W \| pdb_00005f2w	Download File View File

Crystal structure of human KDM4A in complex with compound 16

Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.

(2016) J Med Chem 59: 1388-1409

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	5UP, DMS, EDO, ZN

Explore in 3D

5F32 \| pdb_00005f32	Download File View File

Crystal structure of human KDM4A in complex with compound 40

Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.

(2016) J Med Chem 59: 1388-1409

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	5V7, DMS, EDO, GOL, ZN

Explore in 3D

5F37 \| pdb_00005f37	Download File View File

Crystal structure of human KDM4A in complex with compound 58

Le Bihan, Y.-V., Dempster, S., Westwood, I.M., van Montfort, R.L.M.

(2016) J Med Chem 59: 1388-1409

Released	2016-01-20
Method	X-RAY DIFFRACTION 2.22 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific demethylase 4A (protein)
Unique Ligands	DMS, EDO, N5J, ZN