RCSB PDB: Search

1VGY	Download File View File

Crystal structure of succinyl diaminopimelate desuccinylase

Structural GenomiX

(2005) Proteins 60: 787-796

Released	2003-11-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Neisseria meningitidis MC58
Macromolecule	succinyl-diaminopimelate desuccinylase (protein)

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3IC1	Download File View File

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Nocek, B.P., Gillner, D.M., Holz, R.C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2010) J Mol Biology 397: 617-626

Released	2009-09-22
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Haemophilus influenzae
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	GOL, SO4, ZN

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3ISZ	Download File View File

Crystal structure of mono-zinc form of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Nocek, B.P., Gillner, D.M., Holz, R.C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2010) J Mol Biology 397: 617-626

Released	2009-11-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	SO4, ZN

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3TX8	Download File View File

Crystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution

Joint Center for Structural Genomics (JCSG), Brunger, A.T., Terwilliger, T.C., Read, R.J., Adams, P.D., Levitt, M., Schroder, G.F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 391-403

Released	2011-10-26
Method	X-RAY DIFFRACTION 2.972 Å
Organisms	Corynebacterium glutamicum
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	CL, PO4

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4H2K	Download File View File

Crystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Nocek, B., Jedrzejczak, R., Makowska-Grzyska, M., Starus, A., Holz, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

(2014) PLoS One 9: e93593-e93593

Released	2012-11-21
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Haemophilus influenzae Rd KW20
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	ZN

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4O23	Download File View File

Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58

Nocek, B., Holz, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2015) Biochemistry 54: 4834-4844

Released	2014-01-15
Method	X-RAY DIFFRACTION 2.09 Å
Organisms	Neisseria meningitidis MC58
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	SO4, ZN

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4ONW	Download File View File

Crystal structure of the catalytic domain of DapE protein from V.cholerea

Nocek, B., Makowska-Grzyska, M., Jedrzejczak, R., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2014) PLoS One 9: e93593-e93593

Released	2014-04-23
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Vibrio cholerae O1 biovar El Tor str. N16961
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	ACT, BU1, EDO, GOL

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4OP4	Download File View File

Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form

Nocek, B., Makowska-Grzyska, M., Jedrzejczak, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2014) PLoS One 9: e93593-e93593

Released	2014-04-23
Method	X-RAY DIFFRACTION 1.651 Å
Organisms	Vibrio cholerae O1 biovar El Tor str. N16961
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	BU1, EDO, GOL, ZN

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4PPZ	Download File View File

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58

Nocek, B., Holz, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2015) Biochemistry 54: 4834-4844

Released	2014-03-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Neisseria meningitidis MC58
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	PO4, ZN

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4PQA	Download File View File

Crystal Structure of succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58 in complex with the Inhibitor Captopril

Nocek, B., Starus, A., Holz, R., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

(2015) Biochemistry 54: 4834-4844

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Neisseria meningitidis MC58
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	SO4, X8Z, ZN

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5UEJ	Download File View File

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58

Nocek, B., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2017-02-01
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Neisseria meningitidis
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	SO4, ZN

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5VO3	Download File View File

Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)

Nocek, B.

(2018) Biochemistry 57: 574-584

Released	2018-07-25
Method	X-RAY DIFFRACTION 1.954 Å
Organisms	Haemophilus influenzae
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	API, SIN, ZN

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7LGP	Download File View File

DapE enzyme from Shigella flexneri

Osipiuk, J., Endres, M., Becker, D.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2021-01-27
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Shigella flexneri 2a str. 301
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	CL, NA, ZN

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7T1Q	Download File View File

Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid

Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Pshenychnyi, S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2021-12-15
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Acinetobacter baumannii ATCC 17978
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	ACT, PGE, SIN, ZN

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7UOI	Download File View File

Crystallographic structure of DapE from Enterococcus faecium

Gonzalez-Segura, L., Diaz-Vilchis, A., Terrazas-Lopez, M., Diaz-Sanchez, A.G.

(2024) Int J Biol Macromol 270: 132281-132281

Released	2023-04-12
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Enterococcus faecium 1,231,410
Macromolecule	succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	GOL, ZN

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8F8O	Download File View File

Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic and L-Lactic Acids

Minasov, G., Shuvalova, L., Brunzelle, J.S., Dubrovska, I., Pshenychnyi, S., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID), Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2022-11-30
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Acinetobacter baumannii ATCC 17978
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	2OP, CIT, PG4, PGE, SIN, ZN

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8VKT	Download File View File

Crystallographic structure of dimetalated DapE from Enterococcus faecium

Gonzalez-Segura, L., Diaz-Vilchis, A., Terrazas-Lopez, M., Diaz-Sanchez, A.G.

(2024) Int J Biol Macromol 270: 132281-132281

Released	2024-05-29
Method	X-RAY DIFFRACTION 1.398 Å
Organisms	Enterococcus faecium
Macromolecule	Probable succinyl-diaminopimelate desuccinylase (protein)
Unique Ligands	EDO, GOL, ZN

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AF_AFA0A0H3GXL0F1	Download File

Computed structure model of Probable succinyl-diaminopimelate desuccinylase

AlphaFold DB	AF-A0A0H3GXL0-F1
pLDDT (global)	95.91
Organisms	Klebsiella pneumoniae subsp. pneumoniae HS11286
Macromolecule	Probable succinyl-diaminopimelate desuccinylase (protein)

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AF_AFA0A0H3H1C2F1	Download File

Computed structure model of Succinyl-diaminopimelate desuccinylase

AlphaFold DB	AF-A0A0H3H1C2-F1
pLDDT (global)	97.41
Organisms	Klebsiella pneumoniae subsp. pneumoniae HS11286
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)

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AF_AFA0A133CNA8F1	Download File

Computed structure model of Probable succinyl-diaminopimelate desuccinylase

AlphaFold DB	AF-A0A133CNA8-F1
pLDDT (global)	97.14
Organisms	Enterococcus faecium
Macromolecule	Probable succinyl-diaminopimelate desuccinylase (protein)

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AF_AFA0K8F6F1	Download File

Computed structure model of Succinyl-diaminopimelate desuccinylase

AlphaFold DB	AF-A0K8F6-F1
pLDDT (global)	97.67
Organisms	Burkholderia cenocepacia HI2424
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)

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AF_AFA0KIB5F1	Download File

Computed structure model of Succinyl-diaminopimelate desuccinylase

AlphaFold DB	AF-A0KIB5-F1
pLDDT (global)	97.32
Organisms	Aeromonas hydrophila subsp. hydrophila ATCC 7966
Macromolecule	Succinyl-diaminopimelate desuccinylase (protein)