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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ogilvie, D.J."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Homo sapiens (15)
	Glycine max (4)
	Gallus gallus (1)
	Vicugna pacos (1)

Taxonomy

Eukaryota (20)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (8)
	1.5 - 2.0 (10)
	2.5 - 3.0 (1)

Release Date

	2005 - 2009 (4)
	2015 - 2019 (14)
	2020 - 2024 (2)

Enzyme Classification Name

Hydrolases (18)

Symmetry Type

	Cyclic (14)
	Asymmetric (6)

SCOP Classification

Alpha and beta proteins (a/b) (18)

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1 to 20 of 20 Structures

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1WDP \| pdb_00001wdp	Download File View File

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Kang, Y.N., Adachi, M., Utsumi, S., Mikami, B.

(2005) Biochemistry 44: 5106-5116

Released	2005-04-05
Method	X-RAY DIFFRACTION 1.27 Å
Organisms	Glycine max
Macromolecule	Beta-amylase (protein)
Unique Ligands	SO4

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1WDQ \| pdb_00001wdq	Download File View File

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Kang, Y.N., Adachi, M., Utsumi, S., Mikami, B.

(2005) Biochemistry 44: 5106-5116

Released	2005-04-05
Method	X-RAY DIFFRACTION 1.28 Å
Organisms	Glycine max
Macromolecule	Beta-amylase (protein)
Unique Ligands	SO4
Unique branched monosaccharides	GLC

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1WDR \| pdb_00001wdr	Download File View File

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Kang, Y.N., Adachi, M., Utsumi, S., Mikami, B.

(2005) Biochemistry 44: 5106-5116

Released	2005-04-05
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Glycine max
Macromolecule	Beta-amylase (protein)
Unique Ligands	GLC, SO4
Unique branched monosaccharides	GLC

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1WDS \| pdb_00001wds	Download File View File

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Kang, Y.N., Adachi, M., Utsumi, S., Mikami, B.

(2005) Biochemistry 44: 5106-5116

Released	2005-04-05
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Glycine max
Macromolecule	Beta-amylase (protein)
Unique Ligands	GLC, SO4
Unique branched monosaccharides	BGC, GLC

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6AF5 \| pdb_00006af5	Download File View File

DJ-1 after backsoaking

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	CL, ISN

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6AF7 \| pdb_00006af7	Download File View File

DJ-1 C106S unbound

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	1PE, CL

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6AF9 \| pdb_00006af9	Download File View File

DJ-1 with isatin bound (high concentration)

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.39 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	CL, ISN

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6AFA \| pdb_00006afa	Download File View File

DJ-1 with isatin (low concentration)

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	CL, ISN

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6AFB \| pdb_00006afb	Download File View File

DJ-1 C106S incubated with isatin

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	CL, DMS, ISN

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6AFC \| pdb_00006afc	Download File View File

DJ-1 with compound 4

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	72R, CL

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6AFD \| pdb_00006afd	Download File View File

DJ-1 with compound 6

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	72S, CL

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6AFE \| pdb_00006afe	Download File View File

DJ-1 with compound 7

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	72T, CL

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6AFF \| pdb_00006aff	Download File View File

DJ-1 with compound 8

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	72U, CL

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6AFG \| pdb_00006afg	Download File View File

DJ-1 with compound 9

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	72V

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6AFH \| pdb_00006afh	Download File View File

DJ-1 with compound 10

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	73F, CL

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6AFI \| pdb_00006afi	Download File View File

DJ-1 with compound 11

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	73D, CL

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6AFJ \| pdb_00006afj	Download File View File

DJ-1 with compound 13

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	73G, CL

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6AFL \| pdb_00006afl	Download File View File

DJ-1 with compound 15

Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

(2018) ACS Chem Biol 13: 2783-2793

Released	2018-08-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Protein/nucleic acid deglycase DJ-1 (protein)
Unique Ligands	73H, CL

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7WKI \| pdb_00007wki	Download File View File

Structure of the ultra-affinity complex between CFH and a nanobody

Caaveiro, J.M.M., Yokoo, T., Tsumoto, K.

(2022) J Biological Chem 298: 101962-101962

Released	2022-11-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens Vicugna pacos
Macromolecule	Anti-CFH nanobody (VHH) (protein) Complement factor H (protein)

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8X3H \| pdb_00008x3h	Download File View File

Crystal structure of iron-bound recombinant ovotransferrin N-lobe at 0.93 angstrom resolution

Toyoda, M., Mikami, B., Mizutani, K.

To be published

Released	2023-12-13
Method	X-RAY DIFFRACTION 0.93 Å
Organisms	Gallus gallus
Macromolecule	Ovotransferrin (protein)
Unique Ligands	CO3, FE, GOL

1 to 20 of 20 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.

1WDP | pdb_00001wdp

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

1WDQ | pdb_00001wdq

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

1WDR | pdb_00001wdr

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

1WDS | pdb_00001wds

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

6AF5 | pdb_00006af5

DJ-1 after backsoaking

6AF7 | pdb_00006af7

DJ-1 C106S unbound

6AF9 | pdb_00006af9

DJ-1 with isatin bound (high concentration)

6AFA | pdb_00006afa

DJ-1 with isatin (low concentration)

6AFB | pdb_00006afb

DJ-1 C106S incubated with isatin

6AFC | pdb_00006afc

DJ-1 with compound 4

6AFD | pdb_00006afd

DJ-1 with compound 6

6AFE | pdb_00006afe

DJ-1 with compound 7

6AFF | pdb_00006aff

DJ-1 with compound 8

6AFG | pdb_00006afg

DJ-1 with compound 9

6AFH | pdb_00006afh

DJ-1 with compound 10

6AFI | pdb_00006afi

DJ-1 with compound 11

6AFJ | pdb_00006afj

DJ-1 with compound 13

6AFL | pdb_00006afl

DJ-1 with compound 15

7WKI | pdb_00007wki

Structure of the ultra-affinity complex between CFH and a nanobody

8X3H | pdb_00008x3h

Crystal structure of iron-bound recombinant ovotransferrin N-lobe at 0.93 angstrom resolution

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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

1WDP | pdb_00001wdp

1WDQ | pdb_00001wdq

1WDR | pdb_00001wdr

1WDS | pdb_00001wds

6AF5 | pdb_00006af5

6AF7 | pdb_00006af7

6AF9 | pdb_00006af9

6AFA | pdb_00006afa

6AFB | pdb_00006afb

6AFC | pdb_00006afc

6AFD | pdb_00006afd

6AFE | pdb_00006afe

6AFF | pdb_00006aff

6AFG | pdb_00006afg

6AFH | pdb_00006afh

6AFI | pdb_00006afi

6AFJ | pdb_00006afj

6AFL | pdb_00006afl

7WKI | pdb_00007wki

8X3H | pdb_00008x3h