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

232,829 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: PubMed ID = 16365295

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 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

	Homo sapiens (49)
	Felis catus (2)
	Mus musculus (2)
	synthetic construct (2)
	Caenorhabditis elegans (1)
	Legionella pneumophila str. Paris (1)
	Xenopus laevis (1)
	Xenopus tropicalis (1)

Taxonomy

	Eukaryota (49)
	other sequences (2)
	Bacteria (1)

Experimental Method

	X-RAY DIFFRACTION (46)
	ELECTRON MICROSCOPY (3)

Polymer Entity Type

Protein (49)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (18)
	2.0 - 2.5 (10)
	2.5 - 3.0 (6)
	3.0 - 3.5 (7)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (5)
	2010 - 2014 (9)
	2015 - 2019 (14)
	2020 - 2024 (21)

Enzyme Classification Name

	Transferases (49)
	Ligases (22)
	Hydrolases (3)

Symmetry Type

	Asymmetric (42)
	Cyclic (11)

SCOP Classification

	Alpha and beta proteins (a+b) (30)
	Artifacts (21)
	Small proteins (2)

AllSelected

1 to 25 of 49 Structures

Page 1 of 2

Sort by

Explore in 3D

2ESK	Download File View File

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type

Ozkan, E., Yu, H., Deisenhofer, J.

(2005) Proc Natl Acad Sci U S A 102: 18890-18895

Released	2005-12-06
Method	X-RAY DIFFRACTION 1.36 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

2ESO	Download File View File

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala

Ozkan, E., Yu, H., Deisenhofer, J.

(2005) Proc Natl Acad Sci U S A 102: 18890-18895

Released	2005-12-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

2ESP	Download File View File

Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala

Ozkan, E., Yu, H., Deisenhofer, J.

(2005) Proc Natl Acad Sci U S A 102: 18890-18895

Released	2005-12-06
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	CL, MPD

Explore in 3D

2ESQ	Download File View File

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly

Ozkan, E., Yu, H., Deisenhofer, J.

(2005) Proc Natl Acad Sci U S A 102: 18890-18895

Released	2005-12-06
Method	X-RAY DIFFRACTION 1.44 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

3EB6	Download File View File

Structure of the cIAP2 RING domain bound to UbcH5b

Mace, P.D., Linke, K., Schumacher, F.-R., Smith, C.A., Day, C.L.

(2008) J Biological Chem 283: 31633-31640

Released	2008-09-09
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Homo sapiens Xenopus laevis
Macromolecule	Baculoviral IAP repeat-containing protein 3 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	ZN

Explore in 3D

3JVZ	Download File View File

E2~Ubiquitin-HECT

Souphron, J., Kamadurai, H.B., Schulman, B.A.

(2009) Mol Cell 36: 1095-1102

Released	2010-01-12
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4-like (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

3JW0	Download File View File

E2~Ubiquitin-HECT

Kamadurai, H.B., Schulman, B.A.

(2009) Mol Cell 36: 1095-1102

Released	2010-01-12
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase NEDD4-like (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

3L1Y	Download File View File

Crystal structure of human UBC4 E2 conjugating enzyme

Benirschke, R., Thompson, J.R., Mer, G.

(2010) Structure 18: 955-965

Released	2010-05-05
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

3TGD	Download File View File

Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b

Page, R.C., Amick, J., Misra, S.

To be published

Released	2011-08-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

3UGB	Download File View File

UbcH5c~Ubiquitin Conjugate

Page, R.C., Pruneda, J.N., Klevit, R.E., Misra, S.

(2012) Biochemistry 51: 4175-4187

Released	2012-05-16
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) Ubiquitin-conjugating enzyme E2 D3 (protein)
Unique Ligands	GOL

Explore in 3D

4A49	Download File View File

Structure of phosphoTyr371-c-Cbl-UbcH5B complex

Dou, H., Buetow, L., Hock, A., Sibbet, G.J., Vousden, K.H., Huang, D.T.

(2012) Nat Struct Mol Biol 19: 184-192

Released	2012-01-25
Method	X-RAY DIFFRACTION 2.214 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase CBL (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	K, ZN

Explore in 3D

4DDG	Download File View File

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Juang, Y.C., Sanches, M., Sicheri, F.

(2012) Mol Cell 45: 384-397

Released	2012-02-22
Method	X-RAY DIFFRACTION 3.2987 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 (protein)

Explore in 3D

4DDI	Download File View File

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Juang, Y.C., Sanches, M., Sicheri, F.

(2012) Mol Cell 45: 384-397

Released	2012-02-22
Method	X-RAY DIFFRACTION 3.802 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein) Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 (protein)

Explore in 3D

4LDT	Download File View File

The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub

Wiener, R., DiBello, A.T., Lombardi, P.M., Guzzo, C.M., Zhang, X., Matunis, M.J., Wolberger, C.

(2013) Nat Struct Mol Biol 20: 1033-1039

Released	2013-08-14
Method	X-RAY DIFFRACTION 1.901 Å
Organisms	Caenorhabditis elegans Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin aldehyde (protein) Ubiquitin thioesterase otubain-like (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	EDO, MG

Explore in 3D

4WZ3	Download File View File

Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2

Stogios, P.J., Quaile, A.T., Skarina, T., Nocek, B., Di Leo, R., Yim, V., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2015) Structure 23: 1459-1469

Released	2015-01-07
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens Legionella pneumophila str. Paris
Macromolecule	E3 ubiquitin-protein ligase LubX (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)

Explore in 3D

5D0K	Download File View File

Structure of UbE2D2:RNF165:Ub complex

Wright, J.D., Day, C.L., Mace, P.D.

(2016) Nat Struct Mol Biol 23: 45-52

Released	2015-12-09
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) RING finger protein 165 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	ZN

Explore in 3D

5D0M	Download File View File

Structure of UbE2D2:RNF165:Ub complex

Wright, J.D., Day, C.L., Mace, P.D.

(2016) Nat Struct Mol Biol 23: 45-52

Released	2015-12-09
Method	X-RAY DIFFRACTION 1.913 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) RING finger protein 165 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	PO4, ZN

Explore in 3D

5D1K	Download File View File

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7

Liang, Y.-H., Li, S., Weissman, A.M., Ji, X.

(2015) J Biological Chem 290: 30225-30239

Released	2015-10-28
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF25 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	EDO, OXL, PEG, ZN

Explore in 3D

5D1L	Download File View File

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)

Liang, Y.-H., Li, S., Weissman, A.M., Ji, X.

(2015) J Biological Chem 290: 30225-30239

Released	2015-10-28
Method	X-RAY DIFFRACTION 1.618 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF25 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	OXL, PEG, ZN

Explore in 3D

5D1M	Download File View File

Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)

Liang, Y.-H., Li, S., Weissman, A.M., Ji, X.

(2015) J Biological Chem 290: 30225-30239

Released	2015-10-28
Method	X-RAY DIFFRACTION 1.581 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF25 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	EDO, OXL, PEG, ZN

Explore in 3D

5EDV	Download File View File

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex

Lechtenberg, B.C., Mace, P.D., Sanishvili, R., Riedl, S.J.

(2016) Nature 529: 546-550

Released	2016-01-20
Method	X-RAY DIFFRACTION 3.48 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF31 (protein) Polyubiquitin-B (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	ZN

Explore in 3D

5MNJ	Download File View File

Structure of MDM2-MDMX-UbcH5B-ubiquitin complex

Klejnot, M., Huang, D.T.

(2017) Nat Struct Mol Biol 24: 578-587

Released	2017-05-31
Method	X-RAY DIFFRACTION 2.16 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase Mdm2 (protein) Polyubiquitin-B (protein) Protein Mdm4 (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	SO4, ZN

Explore in 3D

5ULF	Download File View File

Crystal Structure of a UbcH5b~Ub conjugate

Middleton, A.J., Day, C.L., Wright, J.D.

To be published

Released	2017-06-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	GOL

Explore in 3D

5ULH	Download File View File

Structure of RNF165 in complex with a UbcH5b~Ub conjugate

Middleton, A.J., Day, C.L., Wright, J.D.

To be published

Released	2017-06-07
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF165 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	GOL, SCN, ZN

Explore in 3D

5ULK	Download File View File

Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate

Middleton, A.J., Day, C.L., Wright, J.D.

To be published

Released	2017-06-07
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF165 (protein) Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	ZN