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

232,059 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: Chemical ID(s) = NEG

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Chemical Attributes

Help

NOT

Count

Add Subquery

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 3 Structures.

Refinements

Structure Determination Methodology

experimental (3)

Scientific Name of Source Organism

	Thermus thermophilus HB8 (2)
	Escherichia coli (1)
	Escherichia coli K-12 (1)
	Escherichia coli str. K-12 substr. MG1655 (1)
	Haloarcula marismortui (1)
	synthetic construct (1)

Taxonomy

	Bacteria (2)
	Archaea (1)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (3)

Polymer Entity Type

	Protein (3)
	RNA (3)

Refinement Resolution (Å)

	2.5 - 3.0 (2)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (2)

Symmetry Type

Asymmetric (3)

SCOP Classification

	Low resolution protein structures (1)
	Alpha and beta proteins (a+b) (1)
	All alpha proteins (1)
	All beta proteins (1)
	Alpha and beta proteins (a/b) (1)
	Peptides (1)
	Small proteins (1)

AllSelected

1 to 3 of 3 Structures

Page 1 of 1

Sort by

Explore in 3D

2QEX	Download File View File

Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

Schroeder, S.J., Blaha, G.

(2007) Antimicrob Agents Chemother 51: 4462-4465

Released	2008-09-30
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Haloarcula marismortui
Macromolecule	Unique protein chains: 29 Unique nucleic acid chains: 2
Unique Ligands	CD, CL, K, MG, NA, NEG

Explore in 3D

4W2I	Download File View File

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

Polikanov, Y.S., Szal, T., Jiang, F., Gupta, P., Matsuda, R., Shiozuka, M., Steitz, T.A., Vazquez-Laslop, N., Mankin, A.S.

(2014) Mol Cell 56: 541-550

Released	2014-10-15
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli Thermus thermophilus HB8 synthetic construct
Macromolecule	Unique protein chains: 49 Unique nucleic acid chains: 6
Unique Ligands	K, MG, NEG, SF4, ZN

Explore in 3D

4WF1	Download File View File

Crystal structure of the E. coli ribosome bound to negamycin.

Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H.D., Buurman, E.T., Blanchard, S.C.

(2014) Proc Natl Acad Sci U S A 111: 16274-16279

Released	2014-11-05
Method	X-RAY DIFFRACTION 3.09 Å
Organisms	Escherichia coli K-12 Escherichia coli str. K-12 substr. MG1655 Thermus thermophilus HB8
Macromolecule	Unique protein chains: 50 Unique nucleic acid chains: 3
Unique Ligands	MG, NEG, ZN

1 to 3 of 3 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.

All questions and comments will receive a response in a timely manner.

Use this form for questions about RCSB.org and RCSB PDB services.
Please attach a screenshot when reporting an issue, if possible.
To update/release your in-progress structure depositions:
access the OneDep Communication panel
For questions/corrections to specific PDB entries, including citation updates:
email deposit-help@mail.wwpdb.org

First Name

Last Name

Subject

Question, Comment, Feedback or Other

Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)

I agree to the Help Desk Privacy Policy

Optional: To help us learn more about our users, what is your:

Institution Type

Role

Main Research Interest

Thank you for providing your feedback! Someone will be in touch with you shortly. This window will automatically close in 5 seconds.

Apologies, our feedback server is currently unavailable and we are troubleshooting the issue. In the meantime, please copy and paste the below information into an email addressed to info@rcsb.org

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

Symmetry Type

SCOP Classification

2QEX

Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

4W2I

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

4WF1

Crystal structure of the E. coli ribosome bound to negamycin.