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

234,136 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 "TRANSFERASE, 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 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Homo sapiens (4)
	Saccharomyces cerevisiae (2)
	Saccharomyces cerevisiae S288C (2)
	Arabidopsis thaliana (1)
	Lactiplantibacillus plantarum WCFS1 (1)
	Legionella pneumophila (1)
	Mycobacterium tuberculosis H37Rv (1)
	Pseudomonas syringae pv. tomato (1)
	Shigella flexneri (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (9)
	Bacteria (5)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (10)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (11)
	DNA (1)

Refinement Resolution (Å)

	2.0 - 2.5 (4)
	2.5 - 3.0 (5)
	3.0 - 3.5 (1)
	3.5 - 4.0 (1)

Release Date

	2010 - 2014 (3)
	2015 - 2019 (2)
	2020 - 2024 (6)

Enzyme Classification Name

	Transferases (9)
	Ligases (4)
	Lyases (1)

Symmetry Type

	Asymmetric (8)
	Cyclic (3)

SCOP Classification

	Alpha and beta proteins (a+b) (2)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 11 of 11 Structures

Page 1 of 1

Sort by

Explore in 3D

3TL8 \| pdb_00003tl8	Download File View File

The AvrPtoB-BAK1 complex reveals two structurally similar kinaseinteracting domains in a single type III effector

Chai, J., Cheng, W., Gao, H.

(2011) Cell Host Microbe 10: 616-626

Released	2012-01-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Arabidopsis thaliana Pseudomonas syringae pv. tomato
Macromolecule	BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 (protein) Effector protein HopAB2 (protein)

Explore in 3D

4ISB \| pdb_00004isb	Download File View File

Crystal Structure of Apo Mtb FadD10

Liu, Z., Wang, F., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

(2013) J Biological Chem 288: 18473-18483

Released	2013-05-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	Long chain fatty acid CoA ligase FadD10 (protein)
Unique Ligands	SO4

Explore in 3D

5W87 \| pdb_00005w87	Download File View File

Crystal structure of the C-terminal lobe of the human HERC6 HECT domain

WANG, Y., BELLESIS, A.G., ROYER, W.E., SPRATT, D.E.

To be published

Released	2018-07-04
Method	X-RAY DIFFRACTION 2.199 Å
Organisms	Homo sapiens
Macromolecule	Probable E3 ubiquitin-protein ligase HERC6 (protein)
Unique Ligands	PO4

Explore in 3D

7MIS \| pdb_00007mis	Download File View File

Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex

Osinski, A., Black, M.H., Pawlowski, K., Chen, Z., Li, Y., Tagliabracci, V.S.

(2021) Mol Cell 81: 4527

Released	2021-08-18
Method	ELECTRON MICROSCOPY 2.8 Å
Organisms	Homo sapiens Legionella pneumophila
Macromolecule	Calmodulin (protein) Calmodulin-dependent glutamylase SidJ (protein) SdeC (protein)
Unique Ligands	AMP, ATP, CA, MG, NA

Explore in 3D

7UV8 \| pdb_00007uv8	Download File View File

Rad6-Bre1 Complex

Shukla, P.K., Chandrasekharan, M.B.

(2023) Nucleic Acids Res 51: 2117-2136

Released	2023-01-11
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	E3 ubiquitin-protein ligase BRE1 (protein) Ubiquitin-conjugating enzyme E2 2 (protein)

Explore in 3D

7UVC \| pdb_00007uvc	Download File View File

Rad6(P43L)-Bre1 Complex

Shukla, P.K., Chandrasekharan, M.B.

(2023) Nucleic Acids Res 51: 2117-2136

Released	2023-01-11
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	E3 ubiquitin-protein ligase BRE1 (protein) Ubiquitin-conjugating enzyme E2 2 (protein)

Explore in 3D

8GRE \| pdb_00008gre	Download File View File

F-box protein in complex with skp1(FL) and substrate

Nishio, K., Nakatsukasa, K., Kamura, T., Mizushima, T.

(2023) Sci Adv 9: eadf1956-eadf1956

Released	2023-04-26
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Citrate synthase (protein) E3 ubiquitin ligase complex SCF subunit (protein) F-box protein UCC1 (protein)
Unique Ligands	GOL

Explore in 3D

8GRF \| pdb_00008grf	Download File View File

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

Nishio, K., Nakatsukasa, K., Kamura, T., Mizushima, T.

(2023) Sci Adv 9: eadf1956-eadf1956

Released	2023-04-26
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Citrate synthase (protein) E3 ubiquitin ligase complex SCF subunit (protein) F-box protein UCC1 (protein)
Unique Ligands	EDO

Explore in 3D

8IE2 \| pdb_00008ie2	Download File View File

Crystal structure of Lactiplantibacillus plantarum GlyRS

Yamashita, S., Tomita, K.

(2023) J Biochem 174: 291-303

Released	2023-06-07
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Lactiplantibacillus plantarum WCFS1
Macromolecule	Glycine--tRNA ligase alpha subunit (protein) Glycine--tRNA ligase beta subunit (protein)

Explore in 3D

5BPC \| pdb_00005bpc	Download File View File

DNA polymerase beta ternary complex with a templating 5ClC and incoming dATP analog

Freudenthal, B.D., Wilson, S.H.

(2015) Proc Natl Acad Sci U S A 112: E4571-E4580

Released	2015-08-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	DNA polymerase beta (protein) DNA (5'-D(CPCPGPAPCP(CDO)PGPCPGPCPAPTPCPAPGPC)-3') (nucleic acid) DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3') (nucleic acid) DNA (5'-D(PGPTPCPGP*G)-3') (nucleic acid)
Unique Ligands	F2A, MN, NA

Explore in 3D

4BVU \| pdb_00004bvu	Download File View File

Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate

Pruneda, J.N., LeTrong, I., Stenkamp, R.E., Klevit, R.E., Brzovic, P.S.

(2014) EMBO J 33: 437

Released	2014-01-29
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens Shigella flexneri
Macromolecule	PROTEIN KINASE OSPG (protein) UBIQUITIN (protein) UBIQUITIN-CONJUGATING ENZYME E2 D3 (protein)

1 to 11 of 11 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.

3TL8 | pdb_00003tl8

The AvrPtoB-BAK1 complex reveals two structurally similar kinaseinteracting domains in a single type III effector

4ISB | pdb_00004isb

Crystal Structure of Apo Mtb FadD10

5W87 | pdb_00005w87

Crystal structure of the C-terminal lobe of the human HERC6 HECT domain

7MIS | pdb_00007mis

Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex

7UV8 | pdb_00007uv8

Rad6-Bre1 Complex

7UVC | pdb_00007uvc

Rad6(P43L)-Bre1 Complex

8GRE | pdb_00008gre

F-box protein in complex with skp1(FL) and substrate

8GRF | pdb_00008grf

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

8IE2 | pdb_00008ie2

Crystal structure of Lactiplantibacillus plantarum GlyRS

5BPC | pdb_00005bpc

DNA polymerase beta ternary complex with a templating 5ClC and incoming dATP analog

4BVU | pdb_00004bvu

Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate

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

3TL8 | pdb_00003tl8

4ISB | pdb_00004isb

5W87 | pdb_00005w87

7MIS | pdb_00007mis

7UV8 | pdb_00007uv8

7UVC | pdb_00007uvc

8GRE | pdb_00008gre

8GRF | pdb_00008grf

8IE2 | pdb_00008ie2

5BPC | pdb_00005bpc

4BVU | pdb_00004bvu