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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 6.2.1.54

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This query matches 10 Structures.

Refinements

Structure Determination Methodology

experimental (10)

Scientific Name of Source Organism

	Bacillus cereus ATCC 14579 (4)
	Bacillus subtilis (2)
	Lactiplantibacillus plantarum subsp. plantarum NC8 (1)
	Staphylococcus aureus subsp. aureus Mu50 (1)
	Streptococcus pyogenes M1 GAS (1)
	Streptococcus pyogenes serotype M6 (1)

Taxonomy

Bacteria (10)

Experimental Method

X-RAY DIFFRACTION (10)

Polymer Entity Type

Protein (10)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (5)
	2.5 - 3.0 (3)

Release Date

	2005 - 2009 (5)
	2010 - 2014 (3)
	2020 - 2024 (2)

Enzyme Classification Name

Ligases (10)

Symmetry Type

Asymmetric (10)

SCOP Classification

	Multi-domain proteins (alpha and beta) (8)
	Artifacts (5)

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1 to 10 of 10 Structures

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Explore in 3D

3DHV \| pdb_00003dhv	Download File View File

Crystal structure of DltA protein in complex with D-alanine adenylate

Du, L., He, Y., Luo, Y.

(2008) Biochemistry 47: 11473-11480

Released	2008-11-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacillus cereus ATCC 14579
Macromolecule	D-alanine-poly(phosphoribitol) ligase (protein)
Unique Ligands	AMP, DAL

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3E7W \| pdb_00003e7w	Download File View File

Crystal structure of DLTA: Implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains

Yonus, H., Neumann, P., Zimmermann, S., May, J.J., Marahiel, M.A., Stubbs, M.T.

(2008) J Biological Chem 283: 32484-32491

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Bacillus subtilis
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)
Unique Ligands	AMP, PO4

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3E7X \| pdb_00003e7x	Download File View File

Crystal structure of DLTA: implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains

Yonus, H., Neumann, P., Zimmermann, S., May, J.J., Marahiel, M.A., Stubbs, M.T.

(2008) J Biological Chem 283: 32484-32491

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)
Unique Ligands	AMP

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3FCC \| pdb_00003fcc	Download File View File

CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH ATP and MAGNESIUM

Osman, K.T., Du, L., He, Y., Luo, Y.

(2009) J Mol Biology 388: 345-355

Released	2009-04-14
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Bacillus cereus ATCC 14579
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)
Unique Ligands	ATP, MG

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3FCE \| pdb_00003fce	Download File View File

Crystal Structure of Bacillus cereus D-alanyl Carrier Protein Ligase DltA in Complex with ATP: Implications for Adenylation Mechanism

Osman, K.T., Du, L., He, Y., Luo, Y.

(2009) J Mol Biology 388: 345-355

Released	2009-04-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacillus cereus ATCC 14579
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)
Unique Ligands	ATP, CA

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3L8C \| pdb_00003l8c	Download File View File

Structure of probable D-alanine--poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2010-01-19
Method	X-RAY DIFFRACTION 2.41 Å
Organisms	Streptococcus pyogenes serotype M6
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)

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3LGX \| pdb_00003lgx	Download File View File

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2010-03-02
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Streptococcus pyogenes M1 GAS
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)
Unique Ligands	ATP

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4PZP \| pdb_00004pzp	Download File View File

Substrate-free structure of D-alanine carrier protein ligase DltA from Bacillus cereus

Du, L., Atila, M., Luo, Y.

(2014) F1000Res 3: 106-106

Released	2014-11-26
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacillus cereus ATCC 14579
Macromolecule	D-alanine--poly(phosphoribitol) ligase subunit 1 (protein)

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7R27 \| pdb_00007r27	Download File View File

Crystal structure of the L. plantarum D-alanine ligase DltA

Nikolopoulos, N., Ravaud, S., Simorre, J.P., Grangeasse, C.

(2022) Sci Rep 12: 13133-13133

Released	2022-08-03
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Lactiplantibacillus plantarum subsp. plantarum NC8
Macromolecule	D-alanine--D-alanyl carrier protein ligase (protein)
Unique Ligands	AMP, DAL

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7VHV \| pdb_00007vhv	Download File View File

Crystal structure of S. aureus D-alanine alanyl carrier protein ligase

Lee, B.J., Lee, I.-G., Im, H.G., Yoon, H.J.

(2022) Acta Crystallogr D Struct Biol 78: 424-434

Released	2022-04-13
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Staphylococcus aureus subsp. aureus Mu50
Macromolecule	D-alanine--D-alanyl carrier protein ligase (protein)
Unique Ligands	ATP, MG

1 to 10 of 10 Structures

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3DHV | pdb_00003dhv

Crystal structure of DltA protein in complex with D-alanine adenylate

3E7W | pdb_00003e7w

Crystal structure of DLTA: Implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains

3E7X | pdb_00003e7x

Crystal structure of DLTA: implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains

3FCC | pdb_00003fcc

CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH ATP and MAGNESIUM

3FCE | pdb_00003fce

Crystal Structure of Bacillus cereus D-alanyl Carrier Protein Ligase DltA in Complex with ATP: Implications for Adenylation Mechanism

3L8C | pdb_00003l8c

Structure of probable D-alanine--poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes

3LGX | pdb_00003lgx

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

4PZP | pdb_00004pzp

Substrate-free structure of D-alanine carrier protein ligase DltA from Bacillus cereus

7R27 | pdb_00007r27

Crystal structure of the L. plantarum D-alanine ligase DltA

7VHV | pdb_00007vhv

Crystal structure of S. aureus D-alanine alanyl carrier protein ligase

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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

3DHV | pdb_00003dhv

3E7W | pdb_00003e7w

3E7X | pdb_00003e7x

3FCC | pdb_00003fcc

3FCE | pdb_00003fce

3L8C | pdb_00003l8c

3LGX | pdb_00003lgx

4PZP | pdb_00004pzp

7R27 | pdb_00007r27

7VHV | pdb_00007vhv