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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Actinomadura sp. R39"

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Search Summary

This query matches 18 Structures.

Refinements

Structure Determination Methodology

experimental (18)

Scientific Name of Source Organism

Actinomadura sp. R39 (18)

Taxonomy

Bacteria (18)

Experimental Method

X-RAY DIFFRACTION (18)

Polymer Entity Type

Protein (18)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (9)
	2.5 - 3.0 (7)
	3.0 - 3.5 (1)

Release Date

	2005 - 2009 (6)
	2010 - 2014 (12)

Enzyme Classification Name

Hydrolases (18)

Symmetry Type

Asymmetric (18)

SCOP Classification

Multi-domain proteins (alpha and beta) (17)

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1 to 18 of 18 Structures

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1W79 \| pdb_00001w79	Download File View File

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39

Sauvage, E., Herman, R., Petrella, S., Duez, C., Frere, J.M., Charlier, P.

(2005) J Biological Chem 280: 31249-31256

Released	2005-06-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-alanyl-D-alanine carboxypeptidase (protein)
Unique Ligands	MG, SO4

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1W8Q \| pdb_00001w8q	Download File View File

Crystal Structure of the DD-Transpeptidase-carboxypeptidase from Actinomadura R39

Sauvage, E., Herman, R., Petrella, S., Duez, C., Frere, J.M., Charlier, P.

(2005) J Biological Chem 280: 31249

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	CO, SO4

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1W8Y \| pdb_00001w8y	Download File View File

Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.

Sauvage, E., Herman, R., Petrella, S., Duez, C., Frere, J.M., Charlier, P.

(2005) J Biological Chem 280: 31249

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-alanyl-D-alanine carboxypeptidase (protein)
Unique Ligands	MG, NCF, SO4

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2VGJ \| pdb_00002vgj	Download File View File

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

Sauvage, E., kerff, F., Herman, R., Charlier, P.

(2008) J Mol Biology 381: 383

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	MG, REC, SO4

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2VGK \| pdb_00002vgk	Download File View File

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

Sauvage, E., kerff, F., Herman, R., Charlier, P.

(2008) J Mol Biology 381: 383

Released	2008-11-25
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	MG, REZ, SO4

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2WKE \| pdb_00002wke	Download File View File

Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate.

Sauvage, E., Herman, R., Kerff, F., Charlier, P.

(2009) J Am Chem Soc 131: 15262

Released	2009-12-01
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	BIY, CO, SO4

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2XDM \| pdb_00002xdm	Download File View File

Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor

Rocaboy, M., Sauvage, E., Herman, R., Kerff, F., Charlier, P.

(2010) Biochemistry 49: 6411

Released	2010-07-21
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	BO8, CO, MES, SO4

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2XK1 \| pdb_00002xk1	Download File View File

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) ACS Med Chem Lett 2: 219

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	CO, EWB, SO4

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2XLN \| pdb_00002xln	Download File View File

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) ACS Med Chem Lett 2: 219

Released	2011-01-26
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, (protein)
Unique Ligands	CO, EWA, SO4

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2Y4A \| pdb_00002y4a	Download File View File

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Sauvage, E., Zervosen, A., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) J Am Chem Soc 133: 10839

Released	2011-07-27
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	BH6, MG, SO4

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2Y55 \| pdb_00002y55	Download File View File

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Sauvage, E., Zervosen, A., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) J Am Chem Soc 133: 10839

Released	2011-07-27
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	ACN, FP5, MG, SO4

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2Y59 \| pdb_00002y59	Download File View File

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Sauvage, E., Zervosen, A., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) J Am Chem Soc 133: 10839

Released	2011-07-27
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	MG, SO4, ZA3

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3ZCZ \| pdb_00003zcz	Download File View File

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2013) Biochemistry 52: 2128

Released	2013-03-27
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	MG, SO4, TFR

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3ZVT \| pdb_00003zvt	Download File View File

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Sauvage, E., Zervosen, A., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) J Am Chem Soc 133: 10839

Released	2012-02-29
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	B07, MG, SO4

Explore in 3D

3ZVW \| pdb_00003zvw	Download File View File

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Sauvage, E., Zervosen, A., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

(2011) J Am Chem Soc 133: 10839

Released	2012-02-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	33D, ACN, FP5, MES, MG, SO4

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4B4X \| pdb_00004b4x	Download File View File

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor

Cannella, S.E., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

To be published

Released	2013-08-21
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	HQZ, MG, SO4

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4B4Z \| pdb_00004b4z	Download File View File

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor

Cannella, S.E., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

To be published

Released	2013-08-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	BSF, MG, SO4

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4BEN \| pdb_00004ben	Download File View File

R39-imipenem Acyl-enzyme crystal structure

Van Elder, D., Sauvage, E., Herman, R., Kerff, F., Rocaboy, M., Charlier, P.

To be published

Released	2013-03-20
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Actinomadura sp. R39
Macromolecule	D-ALANYL-D-ALANINE CARBOXYPEPTIDASE (protein)
Unique Ligands	GOL, IM2, MES, MG, SO4

1 to 18 of 18 Structures

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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.

1W79 | pdb_00001w79

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39

1W8Q | pdb_00001w8q

Crystal Structure of the DD-Transpeptidase-carboxypeptidase from Actinomadura R39

1W8Y | pdb_00001w8y

Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.

2VGJ | pdb_00002vgj

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

2VGK | pdb_00002vgk

Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin

2WKE | pdb_00002wke

Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate.

2XDM | pdb_00002xdm

Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor

2XK1 | pdb_00002xk1

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

2XLN | pdb_00002xln

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a boronate inhibitor

2Y4A | pdb_00002y4a

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

2Y55 | pdb_00002y55

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

2Y59 | pdb_00002y59

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

3ZCZ | pdb_00003zcz

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

3ZVT | pdb_00003zvt

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

3ZVW | pdb_00003zvw

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

4B4X | pdb_00004b4x

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor

4B4Z | pdb_00004b4z

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor

4BEN | pdb_00004ben

R39-imipenem Acyl-enzyme crystal structure

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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

1W79 | pdb_00001w79

1W8Q | pdb_00001w8q

1W8Y | pdb_00001w8y

2VGJ | pdb_00002vgj

2VGK | pdb_00002vgk

2WKE | pdb_00002wke

2XDM | pdb_00002xdm

2XK1 | pdb_00002xk1

2XLN | pdb_00002xln

2Y4A | pdb_00002y4a

2Y55 | pdb_00002y55

2Y59 | pdb_00002y59

3ZCZ | pdb_00003zcz

3ZVT | pdb_00003zvt

3ZVW | pdb_00003zvw

4B4X | pdb_00004b4x

4B4Z | pdb_00004b4z

4BEN | pdb_00004ben