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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Bonomo, R.A."

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Corynebacterium glutamicum (5)
	Ureibacillus thermosphaericus (5)
	Clostridium tetani E88 (4)
	Symbiobacterium thermophilum IAM 14863 (3)
	Hoylesella timonensis (2)
	Proteus vulgaris (2)
	Bacillus thermozeamaize (1)
	Corynebacterium glutamicum ATCC 13032 (1)
	Porphyromonas gingivalis W83 (1)

Taxonomy

Bacteria (24)

Experimental Method

X-RAY DIFFRACTION (24)

Polymer Entity Type

Protein (24)

Refinement Resolution (Å)

	1.5 - 2.0 (7)
	2.0 - 2.5 (14)
	2.5 - 3.0 (1)
	3.0 - 3.5 (2)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (1)
	2005 - 2009 (1)
	2010 - 2014 (7)
	2015 - 2019 (7)
	2020 - 2024 (5)

Enzyme Classification Name

Oxidoreductases (24)

Symmetry Type

	Cyclic (19)
	Dihedral (7)
	Asymmetric (1)

SCOP Classification

	Alpha and beta proteins (a+b) (4)
	Alpha and beta proteins (a/b) (4)

AllSelected

1 to 24 of 24 Structures

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1DAP \| pdb_00001dap	Download File View File

C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+

Scapin, G., Reddy, S.G., Blanchard, J.S.

(1996) Biochemistry 35: 13540-13551

Released	1997-07-07
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Corynebacterium glutamicum
Macromolecule	DIAMINOPIMELIC ACID DEHYDROGENASE (protein)
Unique Ligands	ACT, NDP

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1F06 \| pdb_00001f06	Download File View File

THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE

Cirilli, M., Scapin, G., Sutherland, A., Caplan, J.F., Vederas, J.C., Blanchard, J.S.

(2000) Protein Sci 9: 2034-2037

Released	2001-05-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Corynebacterium glutamicum
Macromolecule	MESO-DIAMINOPIMELATE D-DEHYDROGENASE (protein)
Unique Ligands	2NP, NDP

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2DAP \| pdb_00002dap	Download File View File

C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH DAP

Scapin, G., Cirilli, M., Reddy, S.G., Gao, Y., Vederas, J.C., Blanchard, J.S.

(1998) Biochemistry 37: 3278-3285

Released	1998-04-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Corynebacterium glutamicum
Macromolecule	DIAMINOPIMELIC ACID DEHYDROGENASE (protein)
Unique Ligands	API

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3BIO \| pdb_00003bio	Download File View File

Crystal structure of oxidoreductase (Gfo/Idh/MocA family member) from Porphyromonas gingivalis W83

Nocek, B., Mulligan, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2007-12-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Porphyromonas gingivalis W83
Macromolecule	Oxidoreductase, Gfo/Idh/MocA family (protein)
Unique Ligands	ACT, EPE, GOL

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3DAP \| pdb_00003dap	Download File View File

C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE

Scapin, G., Cirilli, M., Reddy, S.G., Gao, Y., Vederas, J.C., Blanchard, J.S.

(1998) Biochemistry 37: 3278-3285

Released	1998-04-08
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Corynebacterium glutamicum
Macromolecule	DIAMINOPIMELIC ACID DEHYDROGENASE (protein)
Unique Ligands	DA3, NDP

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3WB9 \| pdb_00003wb9	Download File View File

Crystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

(2014) Chembiochem 15: 217-222

Released	2014-03-26
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Symbiobacterium thermophilum IAM 14863
Macromolecule	Diaminopimelate dehydrogenase (protein)
Unique Ligands	GOL

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3WBB \| pdb_00003wbb	Download File View File

Crystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

(2014) Chembiochem 15: 217-222

Released	2014-03-26
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Symbiobacterium thermophilum IAM 14863
Macromolecule	Diaminopimelate dehydrogenase (protein)
Unique Ligands	GOL, NAP

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3WBF \| pdb_00003wbf	Download File View File

Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

(2014) Chembiochem 15: 217-222

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Symbiobacterium thermophilum IAM 14863
Macromolecule	Diaminopimelate dehydrogenase (protein)
Unique Ligands	API, GOL, NAP

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3WGO \| pdb_00003wgo	Download File View File

Crystal structure of Q154L/T173I/R199M/P248S/H249/N276S mutant of meso-dapdh from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published

Released	2014-08-20
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Clostridium tetani E88
Macromolecule	Meso-diaminopimelate dehydrogenase (protein)

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3WGQ \| pdb_00003wgq	Download File View File

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with DAP of from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published

Released	2014-08-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridium tetani E88
Macromolecule	Meso-diaminopimelate dehydrogenase (protein)
Unique Ligands	API

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3WGY \| pdb_00003wgy	Download File View File

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with 4-methyl-2-oxovalerate of from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published

Released	2014-08-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridium tetani E88
Macromolecule	Meso-diaminopimelate dehydrogenase (protein)
Unique Ligands	COI

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3WGZ \| pdb_00003wgz	Download File View File

Crystal structure of meso-dapdh Q154L/T173I/R199M/P248S/H249N/N276S mutant with D-leucine of from Clostridium tetani E88

Liu, W.D., Li, Z., Huang, C.H., Guo, R.T., Wu, Q.Q., Zhu, D.M.

To be published

Released	2014-08-20
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Clostridium tetani E88
Macromolecule	Meso-diaminopimelate dehydrogenase (protein)
Unique Ligands	DLE

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3WYB \| pdb_00003wyb	Download File View File

Structure of a meso-diaminopimelate dehydrogenase

Sakuraba, H., Akita, H., Ohshima, T.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1136-1146

Released	2015-05-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Ureibacillus thermosphaericus
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)

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3WYC \| pdb_00003wyc	Download File View File

Structure of a meso-diaminopimelate dehydrogenase in complex with NADP

Sakuraba, H., Akita, H., Ohshima, T.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1136-1146

Released	2015-05-06
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Ureibacillus thermosphaericus
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	NAP, NES

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5GZ1 \| pdb_00005gz1	Download File View File

Structure of substrate/cofactor-free D-amino acid dehydrogenase

Sakuraba, H., Seto, T., Hayashi, J., Akita, H., Yoneda, K., Ohshima, T.

(2017) Appl Environ Microbiol 83:

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Ureibacillus thermosphaericus
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)

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5GZ3 \| pdb_00005gz3	Download File View File

Structure of D-amino acid dehydrogenase in complex with NADP

Sakuraba, H., Seto, T., Hayashi, J., Akita, H., Yoneda, K., Ohshima, T.

(2017) Appl Environ Microbiol 83:

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Ureibacillus thermosphaericus
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	EDO, NAP

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5GZ6 \| pdb_00005gz6	Download File View File

Structure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid

Sakuraba, H., Seto, T., Hayashi, J., Akita, H., Yoneda, K., Ohshima, T.

(2017) Appl Environ Microbiol 83:

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Ureibacillus thermosphaericus
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	7C3, ACT, NDP, SO4

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5LOA \| pdb_00005loa	Download File View File

Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) bound to NADP+

Dunstan, M.S., Gahloth, D.

To be published

Released	2017-08-16
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Corynebacterium glutamicum ATCC 13032
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	NAP

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5LOC \| pdb_00005loc	Download File View File

Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH)

Dunstan, M.S., Gahloth, D.

To be published

Released	2017-08-16
Method	X-RAY DIFFRACTION 2.04 Å
Organisms	Corynebacterium glutamicum
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)

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8HP0 \| pdb_00008hp0	Download File View File

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis

Tan, Y., Song, W.

(2023) Appl Environ Microbiol 89: e0010923-e0010923

Released	2023-12-13
Method	X-RAY DIFFRACTION 2.47 Å
Organisms	Hoylesella timonensis
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	EPE, SO4

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8HP3 \| pdb_00008hp3	Download File View File

Crystal structure of meso-diaminopimelate dehydrogenase from Prevotella timonensis

Tan, Y., Song, W.

(2023) Appl Environ Microbiol 89: e0010923-e0010923

Released	2023-12-13
Method	X-RAY DIFFRACTION 3.07 Å
Organisms	Hoylesella timonensis
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	EDO, NDP, SO4

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8I78 \| pdb_00008i78	Download File View File

Meso-Diaminopimelate dehydrogenase

Wei, S., Wu, T.F.

To be published

Released	2024-02-07
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Proteus vulgaris
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)

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8I7H \| pdb_00008i7h	Download File View File

Meso-Diaminopimelate dehydrogenase

Wu, T.F., Song, W.

To be published

Released	2024-02-07
Method	X-RAY DIFFRACTION 3.02 Å
Organisms	Proteus vulgaris
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	API, SO4

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8ZMX \| pdb_00008zmx	Download File View File

Crystal Structures of meso-diaminopimelate dehydrogenase from Bacillus thermozeamaize

Geng, Q., Wei, Y., Zhang, Z.J.

(2024) ACS Catal 14: 11447-11456

Released	2024-11-13
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Bacillus thermozeamaize
Macromolecule	Meso-diaminopimelate D-dehydrogenase (protein)
Unique Ligands	NAP

1 to 24 of 24 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

1DAP | pdb_00001dap

1F06 | pdb_00001f06

2DAP | pdb_00002dap

3BIO | pdb_00003bio

3DAP | pdb_00003dap

3WB9 | pdb_00003wb9

3WBB | pdb_00003wbb

3WBF | pdb_00003wbf

3WGO | pdb_00003wgo

3WGQ | pdb_00003wgq

3WGY | pdb_00003wgy

3WGZ | pdb_00003wgz

3WYB | pdb_00003wyb

3WYC | pdb_00003wyc

5GZ1 | pdb_00005gz1

5GZ3 | pdb_00005gz3

5GZ6 | pdb_00005gz6

5LOA | pdb_00005loa

5LOC | pdb_00005loc

8HP0 | pdb_00008hp0

8HP3 | pdb_00008hp3

8I78 | pdb_00008i78

8I7H | pdb_00008i7h

8ZMX | pdb_00008zmx