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

233,605 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: Source Organism Taxonomy Name (Full Lineage) = "Escherichia coli str. K-12 substr. W3110"

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 33 Structures.

Refinements

Structure Determination Methodology

experimental (33)

Scientific Name of Source Organism

	Escherichia coli str. K-12 substr. W3110 (33)
	Escherichia coli (4)
	Escherichia coli K-12 (1)
	synthetic construct (1)

Taxonomy

	Bacteria (33)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (31)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (33)
	DNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (9)
	2.0 - 2.5 (12)
	2.5 - 3.0 (5)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (3)
	2000 - 2004 (6)
	2005 - 2009 (19)
	2010 - 2014 (4)

Enzyme Classification Name

	Hydrolases (11)
	Transferases (5)
	Oxidoreductases (4)
	Ligases (3)
	Lyases (1)

Membrane Protein Annotation

	MemProtMD (2)
	OPM (2)
	PDBTM (2)
	mpstruc (2)

Symmetry Type

	Asymmetric (19)
	Cyclic (14)
	Dihedral (6)

SCOP Classification

	Alpha and beta proteins (a+b) (12)
	Alpha and beta proteins (a/b) (12)
	All alpha proteins (10)
	All beta proteins (3)
	Artifacts (1)
	Coiled coil proteins (1)

AllSelected

1 to 25 of 33 Structures

Page 1 of 2

Sort by

Explore in 3D

1GZ5 \| pdb_00001gz5	Download File View File

Trehalose-6-phosphate synthase. OtsA

Gibson, R.P., Turkenburg, J.P., Davies, G.J.

(2002) Chem Biol 9: 1337

Released	2003-02-07
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	ALPHA-TREHALOSE-PHOSPHATE SYNTHASE (protein)
Unique Ligands	G6P, IMD, UDP

Explore in 3D

1H9C \| pdb_00001h9c	Download File View File

NMR structure of cysteinyl-phosphorylated enzyme IIB of the N,N'-diacetylchitobiose specific phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli.

Ab, E., Schuurman-Wolters, G.K., Nijlant, D., Dijkstra, K., Saier, M.H., Robillard, G.T., Scheek, R.M.

(2001) J Mol Biology 308: 993-1009

Released	2001-05-21
Method	SOLUTION NMR
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	PTS SYSTEM, CHITOBIOSE-SPECIFIC IIB COMPONENT (protein)

Explore in 3D

1JCH \| pdb_00001jch	Download File View File

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

Soelaiman, S., Jakes, K., Wu, N., Li, C., Shoham, M.

(2001) Mol Cell 8: 1053-1062

Released	2001-11-30
Method	X-RAY DIFFRACTION 3.02 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	COLICIN E3 (protein) COLICIN E3 IMMUNITY PROTEIN (protein)
Unique Ligands	CIT, GOL

Explore in 3D

1M08 \| pdb_00001m08	Download File View File

Crystal structure of the unbound nuclease domain of ColE7

Cheng, Y.S., Hsia, K.C., Doudeva, L.G., Chak, K.F., Yuan, H.S.

(2002) J Mol Biology 324: 227-236

Released	2002-12-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein)
Unique Ligands	PO4, ZN

Explore in 3D

1P7T \| pdb_00001p7t	Download File View File

Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom resolution

Anstrom, D.M., Kallio, K., Remington, S.J.

(2003) Protein Sci 12: 1822-1832

Released	2003-09-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Malate synthase G (protein)
Unique Ligands	ACO, MG, PEG, PG4, PYR

Explore in 3D

1PT3 \| pdb_00001pt3	Download File View File

Crystal structures of nuclease-ColE7 complexed with octamer DNA

Hsia, K.C., Chak, K.F., Cheng, Y.S., Ku, W.Y., Yuan, H.S.

(2004) Structure 12: 205-214

Released	2004-03-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein) 5'-GCGATCGC-3' (nucleic acid)

Explore in 3D

1Q2L \| pdb_00001q2l	Download File View File

Crystal Structure of pitrilysin

Maskos, K., Jozic, D., Fernandez-Catalan, C.

To be published

Released	2005-05-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Protease III (protein)
Unique Ligands	PT, ZN

Explore in 3D

1RNL \| pdb_00001rnl	Download File View File

THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL FROM NARL

Baikalov, I., Schroder, I., Kaczor-Grzeskowiak, M., Grzeskowiak, K., Gunsalus, R.P., Dickerson, R.E.

(1996) Biochemistry 35: 11053-11061

Released	1996-11-08
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL (protein)
Unique Ligands	GOL, PT

Explore in 3D

1TRO \| pdb_00001tro	Download File View File

CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION

Otwinowski, Z., Schevitz, R.W., Zhang, R.-G., Lawson, C.L., Joachimiak, A., Marmorstein, R., Luisi, B.F., Sigler, P.B.

(1988) Nature 335: 321-329

Released	1994-01-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	PROTEIN (TRP REPRESSOR) (protein) DNA (5'-D(TPGPTPAPCPTPAPGPTPTPAPAPCPTPAPGPT PAP*C)-3') (nucleic acid)
Unique Ligands	TRP

Explore in 3D

1VRS \| pdb_00001vrs	Download File View File

Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD

Rozhkova, A., Stirnimann, C.U., Frei, P., Grauschopf, U., Brunisholz, R., Gruetter, M.G., Capitani, G., Glockshuber, R.

(2004) EMBO J 23: 1709-1719

Released	2005-07-12
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Thiol:disulfide interchange protein dsbD (protein)

Explore in 3D

1WQ3 \| pdb_00001wq3	Download File View File

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with 3-iodo-L-tyrosine

Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proc Natl Acad Sci U S A 102: 1366-1371

Released	2005-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	IYR

Explore in 3D

1WQ4 \| pdb_00001wq4	Download File View File

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with L-tyrosine

Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2005) Proc Natl Acad Sci U S A 102: 1366-1371

Released	2005-01-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	TYR

Explore in 3D

1ZNS \| pdb_00001zns	Download File View File

Crystal structure of N-ColE7/12-bp DNA/Zn complex

Doudeva, L.G., Huang, H., Hsia, K.C., Shi, Z., Li, C.L., Shen, Y., Yuan, H.S.

(2006) Protein Sci 15: 269-280

Released	2006-03-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein) 5'-D(CPGPGPGPAPTPAPTPCPCPCPG)-3' (nucleic acid)
Unique Ligands	ZN

Explore in 3D

1ZNV \| pdb_00001znv	Download File View File

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor

Doudeva, L.G., Huang, H., Hsia, K.C., Shi, Z., Li, C.L., Shen, Y., Yuan, H.S.

(2006) Protein Sci 15: 269-280

Released	2006-03-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein) Colicin E7 immunity protein (protein)
Unique Ligands	NI, PO4

Explore in 3D

2AXC \| pdb_00002axc	Download File View File

Crystal structure of ColE7 translocation domain

Cheng, Y.S., Shi, Z., Doudeva, L.G., Yang, W.Z., Chak, K.F., Yuan, H.S.

(2006) J Mol Biology 356: 22-31

Released	2006-03-14
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Colicin E7 (protein)
Unique Ligands	GOL, SO4

Explore in 3D

2DHM \| pdb_00002dhm	Download File View File

Solution structure of the BolA protein from Escherichia coli

Kasai, T., Kigawa, T., Koshiba, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2006-09-24
Method	SOLUTION NMR
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Protein bolA (protein)

Explore in 3D

2EGH \| pdb_00002egh	Download File View File

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with a magnesium ion, NADPH and fosmidomycin

Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Seto, H.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 466-470

Released	2007-06-19
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	1-deoxy-D-xylulose 5-phosphate reductoisomerase (protein)
Unique Ligands	FOM, MG, NDP

Explore in 3D

2FHS \| pdb_00002fhs	Download File View File

Structure of Acyl Carrier Protein Bound to FabI, the Enoyl Reductase from Escherichia Coli

Kolappan, S., Novichenok, P., Rafi, S., Simmerling, C., Tonge, P.J., Kisker, C.

(2006) J Biological Chem 281: 39285-39293

Released	2006-10-17
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Escherichia coli Escherichia coli str. K-12 substr. W3110
Macromolecule	Acyl carrier protein (protein) enoyl-[acyl-carrier-protein] reductase, NADH-dependent (protein)

Explore in 3D

2IV7 \| pdb_00002iv7	Download File View File

Crystal Structure of WaaG, a glycosyltransferase involved in lipopolysaccharide biosynthesis

Martinez-Fleites, C., Proctor, M., Roberts, S., Bolam, D.N., Gilbert, H.J., Davies, G.J.

(2006) Chem Biol 13: 1143

Released	2006-10-11
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN RFAG (protein)
Unique Ligands	UDP

Explore in 3D

2IW1 \| pdb_00002iw1	Download File View File

Crystal Structure of WaaG, a glycosyltransferase involved in lipopolysaccharide biosynthesis

Martinez-Fleites, C., Proctor, M., Roberts, S., Bolam, D.N., Gilbert, H.J., Davies, G.J.

(2006) Chem Biol 13: 1143

Released	2006-10-11
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN RFAG (protein)
Unique Ligands	U2F

Explore in 3D

2JAZ \| pdb_00002jaz	Download File View File

CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7

Huang, H., Yuan, H.S.

(2007) J Mol Biology 368: 812

Released	2007-04-03
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	COLICIN E7 (protein) COLICIN E7 IMMUNITY PROTEIN (protein)
Unique Ligands	PO4, ZN

Explore in 3D

2JB0 \| pdb_00002jb0	Download File View File

CRYSTAL STRUCTURE OF THE MUTANT H573A OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7

Huang, H., Yuan, H.S.

(2007) J Mol Biology 368: 812

Released	2007-04-03
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	COLICIN E7 (protein) COLICIN E7 IMMUNITY PROTEIN (protein)
Unique Ligands	ZN

Explore in 3D

2JBG \| pdb_00002jbg	Download File View File

crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7

Huang, H., Yuan, H.S.

(2007) J Mol Biology 368: 812

Released	2007-04-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	COLICIN E7 (protein) COLICIN-E7 IMMUNITY PROTEIN (protein)
Unique Ligands	SO4, ZN

Explore in 3D

2QCP \| pdb_00002qcp	Download File View File

1.0 A Structure of CusF-Ag(I) residues 10-88 from Escherichia coli

Loftin, I.R.

(2007) Protein Sci 16: 2287-2293

Released	2007-10-02
Method	X-RAY DIFFRACTION 1 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Cation efflux system protein cusF (protein)
Unique Ligands	AG, NO3, SO4

Explore in 3D

2YXN \| pdb_00002yxn	Download File View File

Structual basis of azido-tyrosine recognition by engineered bacterial Tyrosyl-tRNA synthetase

Oki, K., Kobayashi, T., Sakamoto, K., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2010) Nucleic Acids Res 38: 3682-3691

Released	2008-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli str. K-12 substr. W3110
Macromolecule	Tyrosyl-tRNA synthetase (protein)
Unique Ligands	AZY

1 to 25 of 33 Structures

Page 1 of 2

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.

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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1GZ5 | pdb_00001gz5

1H9C | pdb_00001h9c

1JCH | pdb_00001jch

1M08 | pdb_00001m08

1P7T | pdb_00001p7t

1PT3 | pdb_00001pt3

1Q2L | pdb_00001q2l

1RNL | pdb_00001rnl

1TRO | pdb_00001tro

1VRS | pdb_00001vrs

1WQ3 | pdb_00001wq3

1WQ4 | pdb_00001wq4

1ZNS | pdb_00001zns

1ZNV | pdb_00001znv

2AXC | pdb_00002axc

2DHM | pdb_00002dhm

2EGH | pdb_00002egh

2FHS | pdb_00002fhs

2IV7 | pdb_00002iv7

2IW1 | pdb_00002iw1

2JAZ | pdb_00002jaz

2JB0 | pdb_00002jb0

2JBG | pdb_00002jbg

2QCP | pdb_00002qcp

2YXN | pdb_00002yxn