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

235,183 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: Structure Keywords HAS EXACT PHRASE "protein binding, ligase"

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 16 Structures.

Refinements

Structure Determination Methodology

experimental (16)

Scientific Name of Source Organism

	Homo sapiens (15)
	Drosophila melanogaster (3)
	Bos taurus (1)
	Schizosaccharomyces pombe (1)

Taxonomy

	Eukaryota (16)
	Eukaryota (eukaryotes) (4)

Experimental Method

X-RAY DIFFRACTION (16)

Polymer Entity Type

Protein (16)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (6)
	2.0 - 2.5 (1)
	2.5 - 3.0 (4)
	3.0 - 3.5 (2)
	4.0 - 4.5 (1)
	> 4.5 (1)

Release Date

	2005 - 2009 (10)
	2010 - 2014 (5)
	2015 - 2019 (1)

Enzyme Classification Name

	Ligases (7)
	Transferases (6)
	Hydrolases (2)

Symmetry Type

	Asymmetric (14)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	All beta proteins (4)
	Alpha and beta proteins (a/b) (1)
	Artifacts (2)

AllSelected

1 to 16 of 16 Structures

Page 1 of 1

Sort by

Explore in 3D

2PE6 \| pdb_00002pe6	Download File View File

Non-covalent complex between human SUMO-1 and human Ubc9

Capili, A.D., Lima, C.D.

(2007) J Mol Biology 369: 608-618

Released	2007-04-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	SUMO-conjugating enzyme UBC9 (protein) Small ubiquitin-related modifier 1 (protein)

Explore in 3D

2QHO \| pdb_00002qho	Download File View File

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin

Kozlov, G., Gehring, K.

(2007) J Biological Chem 282: 35787-35795

Released	2007-09-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase EDD1 (protein) Ubiquitin (protein)

Explore in 3D

3GZN \| pdb_00003gzn	Download File View File

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924

Sintchak, M.D.

(2010) Mol Cell 37: 102-111

Released	2010-02-02
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	NEDD8 (protein) NEDD8-activating enzyme E1 catalytic subunit (protein) NEDD8-activating enzyme E1 regulatory subunit (protein)
Unique Ligands	B39, ZN

Explore in 3D

3HQI \| pdb_00003hqi	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1

Zhuang, M., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.62 Å
Organisms	Homo sapiens
Macromolecule	PucSBC1 (protein) Speckle-type POZ protein (protein)

Explore in 3D

3HQM \| pdb_00003hqm	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2

Zhuang, M., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Drosophila melanogaster Homo sapiens
Macromolecule	Protein cubitus interruptus (protein) Speckle-type POZ protein (protein)
Unique Ligands	SO4

Explore in 3D

3HSV \| pdb_00003hsv	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2

Zhuang, M., Schulman, B.A., Miller, D.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Homo sapiens
Macromolecule	Core histone macro-H2A.1 (protein) Speckle-type POZ protein (protein)
Unique Ligands	SO4, ZN

Explore in 3D

3HTM \| pdb_00003htm	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box

Zhuang, M., Walden, H., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Speckle-type POZ protein (protein)

Explore in 3D

3HU6 \| pdb_00003hu6	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1

Zhuang, M., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Drosophila melanogaster Homo sapiens
Macromolecule	Puckered (protein) Speckle-type POZ protein (protein)

Explore in 3D

3HVE \| pdb_00003hve	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: GigaxoninBTB/3-box

Zhuang, M., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-27
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Gigaxonin (protein)

Explore in 3D

3IVB \| pdb_00003ivb	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

Schulman, B.A., Miller, D.J., Calabrese, M.F., Seyedin, S.

To be published

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Homo sapiens
Macromolecule	Core histone macro-H2A.1 (protein) Speckle-type POZ protein (protein)
Unique Ligands	CL, ZN

Explore in 3D

3PLF \| pdb_00003plf	Download File View File

Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain

Sun, Q., Sivaraman, J.

(2011) FEBS Lett 585: 281-285

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase CBL (protein) MetRD peptide (protein)
Unique Ligands	CA, CL

Explore in 3D

3RCZ \| pdb_00003rcz	Download File View File

Rad60 SLD2 Ubc9 Complex

Perry, J.J.P., Arvai, A.S., Tainer, J.A.

(2011) Mol Cell Biol 31: 2299-2310

Released	2011-04-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Schizosaccharomyces pombe
Macromolecule	DNA repair protein rad60 (protein) SUMO-conjugating enzyme ubc9 (protein)

Explore in 3D

4ORH \| pdb_00004orh	Download File View File

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer

Campbell, S.J., Edwards, R.A., Glover, J.N.M.

(2012) J Biological Chem 287: 23900-23910

Released	2014-02-26
Method	X-RAY DIFFRACTION 4.802 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase RNF8 (protein) Ubiquitin-conjugating enzyme E2 N (protein) Ubiquitin-conjugating enzyme E2 variant 2 (protein)
Unique Ligands	ZN

Explore in 3D

4R3Z \| pdb_00004r3z	Download File View File

Crystal structure of human ArgRS-GlnRS-AIMP1 complex

Fu, Y., Kim, Y., Cho, Y.

(2014) Proc Natl Acad Sci U S A 111: 15084-15089

Released	2014-10-08
Method	X-RAY DIFFRACTION 4.033 Å
Organisms	Homo sapiens
Macromolecule	Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 (protein) Arginine--tRNA ligase, cytoplasmic (protein) Glutamine--tRNA ligase (protein)

Explore in 3D

3HQL \| pdb_00003hql	Download File View File

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2

Zhuang, M., Schulman, B.A.

(2009) Mol Cell 36: 39-50

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.66 Å
Organisms	Drosophila melanogaster Homo sapiens
Macromolecule	Puckered (protein) Speckle-type POZ protein (protein)
Unique Ligands	SO4

Explore in 3D

5H7S \| pdb_00005h7s	Download File View File

Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain

Nayak, D., Sivaraman, J.

(2018) J Mol Biology 430: 1173-1188

Released	2017-11-29
Method	X-RAY DIFFRACTION 3.49 Å
Organisms	Homo sapiens
Macromolecule	E3 ubiquitin-protein ligase LNX (protein) Ubiquitin-conjugating enzyme E2 N (protein) Ubiquitin-like 1 (protein)
Unique Ligands	ZN

1 to 16 of 16 Structures

Page 1 of 1

Sort by

About
About Us
Citing Us
Publications
Team
Careers
Usage & Privacy

Support
Contact Us
Help
Website FAQ
Glossary
Service Status

RCSB PDB is hosted by

RCSB PDB is a member of the

RCSB Partners
Nucleic Acid Knowledgebase

wwPDB Partners
RCSB PDB
PDBe
PDBj
BMRB
EMDB

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.

2PE6 | pdb_00002pe6

Non-covalent complex between human SUMO-1 and human Ubc9

2QHO | pdb_00002qho

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin

3GZN | pdb_00003gzn

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924

3HQI | pdb_00003hqi

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1

3HQM | pdb_00003hqm

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2

3HSV | pdb_00003hsv

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2

3HTM | pdb_00003htm

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPBTB/3-box

3HU6 | pdb_00003hu6

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1

3HVE | pdb_00003hve

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: GigaxoninBTB/3-box

3IVB | pdb_00003ivb

Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1

3PLF | pdb_00003plf

Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain

3RCZ | pdb_00003rcz

Rad60 SLD2 Ubc9 Complex

4ORH | pdb_00004orh

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer

4R3Z | pdb_00004r3z

Crystal structure of human ArgRS-GlnRS-AIMP1 complex

3HQL | pdb_00003hql

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2

5H7S | pdb_00005h7s

Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain

Prepare Data

Validate Data

Deposit Data

Help and Resources

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

2PE6 | pdb_00002pe6

2QHO | pdb_00002qho

3GZN | pdb_00003gzn

3HQI | pdb_00003hqi

3HQM | pdb_00003hqm

3HSV | pdb_00003hsv

3HTM | pdb_00003htm

3HU6 | pdb_00003hu6

3HVE | pdb_00003hve

3IVB | pdb_00003ivb

3PLF | pdb_00003plf

3RCZ | pdb_00003rcz

4ORH | pdb_00004orh

4R3Z | pdb_00004r3z

3HQL | pdb_00003hql

5H7S | pdb_00005h7s