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: Gene Name = "ddlA"

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 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Pseudomonas aeruginosa PAO1 (3)
	Salmonella enterica subsp. enterica serovar Typhimurium (2)
	Xanthomonas oryzae pv. oryzae KACC 10331 (2)
	Mycobacterium tuberculosis (1)
	Staphylococcus aureus (1)

Taxonomy

Bacteria (9)

Experimental Method

X-RAY DIFFRACTION (9)

Polymer Entity Type

Protein (9)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (1)
	2.0 - 2.5 (7)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (4)
	2020 - 2024 (3)

Enzyme Classification Name

Ligases (9)

Symmetry Type

Cyclic (9)

SCOP Classification

	Alpha and beta proteins (a+b) (6)
	Alpha and beta proteins (a/b) (6)
	Artifacts (1)

AllSelected

1 to 9 of 9 Structures

Page 1 of 1

Sort by

Explore in 3D

2I80 \| pdb_00002i80	Download File View File

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

Liu, S., Chang, J.S., Herberg, J.T., Horng, M.-M., Tomich, P.K., Lin, A.H., Marotti, K.R.

(2006) Proc Natl Acad Sci U S A 103: 15178-15183

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Staphylococcus aureus
Macromolecule	D-alanine-D-alanine ligase (protein)
Unique Ligands	G1L

Explore in 3D

3I12 \| pdb_00003i12	Download File View File

The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Zhang, R., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2009-08-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	D-alanine-D-alanine ligase A (protein)
Unique Ligands	ADP

Explore in 3D

3LWB \| pdb_00003lwb	Download File View File

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis

Bruning, J.B., Murillo, A.C., Chacon, O., Barletta, R.G., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

(2011) Antimicrob Agents Chemother 55: 291-301

Released	2010-03-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	NO3

Explore in 3D

3Q1K \| pdb_00003q1k	Download File View File

The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP

Zhang, R., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2011-01-12
Method	X-RAY DIFFRACTION 2.202 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	D-alanine--D-alanine ligase A (protein)
Unique Ligands	ADP, FMT, GOL, MG, SO4

Explore in 3D

4L1K \| pdb_00004l1k	Download File View File

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP

Doan, T.T.N., Kim, J.K., Kang, L.W.

(2014) Arch Biochem Biophys 545C: 92-99

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ANP, MG

Explore in 3D

4ME6 \| pdb_00004me6	Download File View File

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Doan, T.T.N., Kim, J.K., Ahn, Y.J., Lee, B.M., Kang, L.W.

(2014) Arch Biochem Biophys 545C: 92-99

Released	2014-02-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ADP, MG

Explore in 3D

8EVV \| pdb_00008evv	Download File View File

Apo form of DdlA from Pseudomonas aeruginosa PAO1

Pederick, J.L., Woolman, J.C., Bruning, J.B.

(2023) FEBS J 290: 5536-5553

Released	2023-08-30
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	D-alanine--D-alanine ligase A (protein)

Explore in 3D

8EVW \| pdb_00008evw	Download File View File

DdlA from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala

Pederick, J.L., Woolman, J.C., Bruning, J.B.

(2023) FEBS J 290: 5536-5553

Released	2023-08-30
Method	X-RAY DIFFRACTION 1.22 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	D-alanine--D-alanine ligase A (protein)
Unique Ligands	ATP, DAL, MG

Explore in 3D

8EVX \| pdb_00008evx	Download File View File

DdlA from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine

Pederick, J.L., Woolman, J.C., Bruning, J.B.

(2023) FEBS J 290: 5536-5553

Released	2023-08-30
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	D-alanine--D-alanine ligase A (protein)
Unique Ligands	ADP, DS0, K, MG

1 to 9 of 9 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.

2I80 | pdb_00002i80

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

3I12 | pdb_00003i12

The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

3LWB | pdb_00003lwb

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis

3Q1K | pdb_00003q1k

The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP

4L1K | pdb_00004l1k

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with AMPPNP

4ME6 | pdb_00004me6

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

8EVV | pdb_00008evv

Apo form of DdlA from Pseudomonas aeruginosa PAO1

8EVW | pdb_00008evw

DdlA from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala

8EVX | pdb_00008evx

DdlA from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine

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

2I80 | pdb_00002i80

3I12 | pdb_00003i12

3LWB | pdb_00003lwb

3Q1K | pdb_00003q1k

4L1K | pdb_00004l1k

4ME6 | pdb_00004me6

8EVV | pdb_00008evv

8EVW | pdb_00008evw

8EVX | pdb_00008evx