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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "oxalate decarboxylase"

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Mycobacterium tuberculosis H37Rv (18)
	Mycobacterium tuberculosis (11)
	Mycobacterium tuberculosis H37Ra (1)

Taxonomy

Bacteria (30)

Experimental Method

X-RAY DIFFRACTION (30)

Polymer Entity Type

Protein (30)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (16)
	2.0 - 2.5 (10)
	2.5 - 3.0 (2)

Release Date

	2010 - 2014 (10)
	2015 - 2019 (10)
	2020 - 2024 (10)

Enzyme Classification Name

Transferases (29)

Symmetry Type

	Asymmetric (30)
	Cyclic (8)

SCOP Classification

	All beta proteins (19)
	Artifacts (2)

AllSelected

1 to 25 of 30 Structures

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Explore in 3D

3TUR \| pdb_00003tur	Download File View File

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 complexed with a peptidoglycan fragment

Bianchet, M.A., Erdemli, S.B., Gupta, R., Lamichhane, G., Amzel, L.M.

(2012) Structure 20: 2103-2115

Released	2012-12-05
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Mycobacteria Tuberculosis LD-transpeptidase type 2 (protein)
Unique Ligands	0JC, 6CL, DGL, PT

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3TX4 \| pdb_00003tx4	Download File View File

Crystal Structure of Mutant (C354A) M. tuberculosis LD-transpeptidase type 2

Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

(2012) Structure 20: 2103-2115

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Mycobacterium Tuberculosis LD-transpeptidase type 2 (protein)

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3U1P \| pdb_00003u1p	Download File View File

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with Modified Catalytic Cysteine (C354)

Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

(2012) Structure 20: 2103-2115

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Mycobacteria Tuberculosis LD-transpeptidase type 2 (protein)
Unique Ligands	PEG

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3U1Q \| pdb_00003u1q	Download File View File

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with 2-Mercaptoethanol

Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

To be published

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Mycobacteria Tuberculosis LD-transpeptidase type 2 (protein)
Unique Ligands	BME, PEG

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3VAE \| pdb_00003vae	Download File View File

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with Modified Catalytic Cysteine (C354)

Erdemli, S., Bianchet, M.A., Gupta, R., Lamichhane, G., Amzel, L.M.

(2012) Structure 20: 2103-2115

Released	2012-12-12
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	LD-transpeptidase type 2 (protein)
Unique Ligands	PEG

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4GSQ \| pdb_00004gsq	Download File View File

Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains

Kim, H.S., Kim, J., Im, H.N., Yoon, J.Y., An, D.R., Yoon, H.J., Kim, J.Y., Min, H.K., Kim, S.-J., Lee, J.Y., Han, B.W., Suh, S.W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 420-431

Released	2013-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Probable conserved lipoprotein LPPS (protein)
Unique Ligands	CA, GOL

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4GSR \| pdb_00004gsr	Download File View File

Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains

Kim, H.S., Kim, J., Im, H.N., Yoon, J.Y., An, D.R., Yoon, H.J., Kim, J.Y., Min, H.K., Kim, S.-J., Lee, J.Y., Han, B.W., Suh, S.W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 420-431

Released	2013-02-27
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Probable conserved lipoprotein LPPS (protein)
Unique Ligands	EMT, GOL

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4GSU \| pdb_00004gsu	Download File View File

Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains

Kim, H.S., Kim, J., Im, H.N., Yoon, J.Y., An, D.R., Yoon, H.J., Kim, J.Y., Min, H.K., Kim, S.-J., Lee, J.Y., Han, B.W., Suh, S.W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 420-431

Released	2013-02-27
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	Probable conserved lipoprotein LPPS (protein)
Unique Ligands	DWZ

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4HU2 \| pdb_00004hu2	Download File View File

Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain A and B

Both, D., Steiner, E., Lindqvist, Y., Schnell, R., Schneider, G.

(2013) Acta Crystallogr D Biol Crystallogr 69: 432-441

Released	2012-12-12
Method	X-RAY DIFFRACTION 1.46 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	PROBABLE CONSERVED LIPOPROTEIN LPPS (protein)
Unique Ligands	SO4

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4HUC \| pdb_00004huc	Download File View File

Crystal structure of LdtMt2, a L,D-transpeptidase from Mycobacterium tuberculosis: domain B and C

Both, D., Steiner, E., Lindqvist, Y., Schnell, R., Schneider, G.

(2013) Acta Crystallogr D Biol Crystallogr 69: 432-441

Released	2012-12-12
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	PROBABLE CONSERVED LIPOPROTEIN LPPS (protein)
Unique Ligands	ACT, NA

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5DVP \| pdb_00005dvp	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct

Kumar, P., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	DRW, POA, SO4

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5DZJ \| pdb_00005dzj	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation A

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.095 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B7

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5DZP \| pdb_00005dzp	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation B

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-05
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B7

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5E1G \| pdb_00005e1g	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208

Kumar, P., Lamichhane, G., Ginell, S.L.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-12
Method	X-RAY DIFFRACTION 1.852 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	T8G

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5E1I \| pdb_00005e1i	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210

Kumar, P., Ginell, S.L., Lamichhane, G.

(2017) Nat Chem Biol 13: 54-61

Released	2016-10-12
Method	X-RAY DIFFRACTION 2.003 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6B8, GOL, NA

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5K69 \| pdb_00005k69	Download File View File

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224

Lamichhane, G., Ginell, S.L., Kumar, P.

(2017) Nat Chem Biol 13: 54-61

Released	2016-11-09
Method	X-RAY DIFFRACTION 2.001 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	6QR, GOL

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5LB1 \| pdb_00005lb1	Download File View File

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with thionitrobenzoate (TNB) adduct at the active site cysteine-354

Steiner, E.M., Schnell, R., Schneider, G.

(2017) FEBS J 284: 725-741

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	MNB

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6BOI \| pdb_00006boi	Download File View File

Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354

Saavedra, H., Bianchet, M.A.

To be published

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.102 Å
Organisms	Mycobacterium tuberculosis H37Ra
Macromolecule	Putative conserved lipoprotein LppS (protein)
Unique Ligands	E0Y, GOL, PEG, SO4

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6IYV \| pdb_00006iyv	Download File View File

Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ertapenem adduct

Zhao, F., Li, D.F., Wang, D.C.

(2019) Biochem Biophys Res Commun 510: 254-260

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	2RG, GOL, PEG, SO4, TRS

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6IYW \| pdb_00006iyw	Download File View File

Crystal sturucture of L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with Imipenem adduct

Li, D.F., Zhao, F., Wang, D.C.

(2019) Biochem Biophys Res Commun 510: 254-260

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	GOL, IM2

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6LQB \| pdb_00006lqb	Download File View File

A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct

Li, D.F., Qin, Y.L.

(2020) PROG BIOCHEM BIOPHYS 47: 989-997

Released	2021-01-13
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	2RG, ACY, GOL

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7A0Z \| pdb_00007a0z	Download File View File

LppS with covalent adduct derived from 1b

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	BT6, TAM

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7A10 \| pdb_00007a10	Download File View File

LppS with covalent adduct derived from 1g

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	QU5

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7A11 \| pdb_00007a11	Download File View File

LppS with covalent adduct derived from 1E

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	ACT, XL3

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7A1C \| pdb_00007a1c	Download File View File

LdtMT2 with covalent adduct derived from N-Thio-beta-lactam 1a

Schnell, R., Steiner, E.M.

(2021) Cell Chem Biol 28: 1321

Released	2021-04-21
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Mycobacterium tuberculosis H37Rv
Macromolecule	L,D-transpeptidase 2 (protein)
Unique Ligands	DMS

1 to 25 of 30 Structures

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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

3TUR | pdb_00003tur

3TX4 | pdb_00003tx4

3U1P | pdb_00003u1p

3U1Q | pdb_00003u1q

3VAE | pdb_00003vae

4GSQ | pdb_00004gsq

4GSR | pdb_00004gsr

4GSU | pdb_00004gsu

4HU2 | pdb_00004hu2

4HUC | pdb_00004huc

5DVP | pdb_00005dvp

5DZJ | pdb_00005dzj

5DZP | pdb_00005dzp

5E1G | pdb_00005e1g

5E1I | pdb_00005e1i

5K69 | pdb_00005k69

5LB1 | pdb_00005lb1

6BOI | pdb_00006boi

6IYV | pdb_00006iyv

6IYW | pdb_00006iyw

6LQB | pdb_00006lqb

7A0Z | pdb_00007a0z

7A10 | pdb_00007a10

7A11 | pdb_00007a11

7A1C | pdb_00007a1c