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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) = "Aspergillus oryzae RIB40"

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Search Summary

This query matches 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

Aspergillus oryzae RIB40 (49)

Taxonomy

Eukaryota (49)

Experimental Method

X-RAY DIFFRACTION (49)

Polymer Entity Type

Protein (49)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (28)
	2.0 - 2.5 (14)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (5)
	2015 - 2019 (23)
	2020 - 2024 (17)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (19)
	Lyases (5)

Symmetry Type

	Asymmetric (37)
	Cyclic (11)
	Dihedral (2)

SCOP Classification

	All alpha proteins (7)
	Alpha and beta proteins (a/b) (6)
	Alpha and beta proteins (a+b) (2)
	All beta proteins (2)

AllSelected

1 to 25 of 49 Structures

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2PS2 \| pdb_00002ps2	Download File View File

Crystal structure of putative mandelate racemase/muconate lactonizing enzyme from Aspergillus oryzae

Fedorov, A.A., Toro, R., Fedorov, E.V., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2007-05-22
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Putative mandelate racemase/muconate lactonizing enzyme (protein)
Unique Ligands	MG

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3C97 \| pdb_00003c97	Download File View File

Crystal structure of the response regulator receiver domain of a signal transduction histidine kinase from Aspergillus oryzae

Bonanno, J.B., Freeman, J., Bain, K.T., Chang, S., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2008-03-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Signal transduction histidine kinase (protein)

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3Q9T \| pdb_00003q9t	Download File View File

Crystal structure analysis of formate oxidase

Doubayashi, D., Ootake, T., Maeda, Y., Oki, M., Tokunaga, Y., Sakurai, A., Nagaosa, Y., Mikami, B., Uchida, H.

(2011) Biosci Biotechnol Biochem 75: 1662-1667

Released	2011-09-21
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Choline dehydrogenase and related flavoproteins (protein)
Unique Ligands	ACT, FAY, MPD, MRD, PEG

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3SYU \| pdb_00003syu	Download File View File

Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP

Smart, O.S., Womack, T.O., Bricogne, G.

(2012) Acta Crystallogr D Biol Crystallogr 68: 368-380

Released	2012-03-28
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Guanyl-specific ribonuclease T1 (protein)
Unique Ligands	2GP, NA, UNX

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3VX0 \| pdb_00003vx0	Download File View File

Crystal Structure of alpha-amylase from Aspergillus oryzae

Sugahara, M.

To be published

Released	2013-09-11
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Alpha-amylase A type-1/2 (protein)
Unique Ligands	CA, GD, NAG

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3VX1 \| pdb_00003vx1	Download File View File

Crystal Structure of alpha-Amylase from Aspergillus oryzae

Sugahara, M.

To be published

Released	2013-09-11
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Alpha-amylase A type-1/2 (protein)
Unique Ligands	CA, NAG

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3WMT \| pdb_00003wmt	Download File View File

Crystal structure of feruloyl esterase B from Aspergillus oryzae

Suzuki, K., Ishida, T., Igarashi, K., Koseki, T., Fushinobu, S.

(2014) Proteins 82: 2857-2867

Released	2014-08-06
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Probable feruloyl esterase B-1 (protein)
Unique Ligands	CA, NAG

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4OPB \| pdb_00004opb	Download File View File

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae

Lo Leggio, L., Frandsen, K.H., Davies, G.J., Dupree, P., Walton, P., Henrissat, B., Stringer, M., Tovborg, M., De Maria, L., Johansen, K.S.

(2015) Nat Commun 6: 5961-5961

Released	2015-01-28
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Predicted protein (protein)
Unique Ligands	ACT, CU, GOL, IPA, NAG, ZN

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5EO7 \| pdb_00005eo7	Download File View File

Crystal structure of AOL

Kato, R., Kiso, M., Ishida, H., Ando, H., Suzuki, T., Shimabukuro, S., Makyio, H.

(2016) Biochem Biophys Res Commun 477: 477-482

Released	2016-06-29
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Predicted protein (protein)
Unique Ligands	SFU, SO4

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5EO8 \| pdb_00005eo8	Download File View File

Crystal structure of AOL(868)

Kato, R., Kiso, M., Ishida, H., Ando, H., Suzuki, T., Shimabukuro, S., Makyio, H.

(2016) Biochem Biophys Res Commun 477: 477-482

Released	2016-06-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Predicted protein (protein)
Unique Ligands	TFU

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5FB9 \| pdb_00005fb9	Download File View File

S1 nuclease from Aspergillus oryzae with unoccupied active site

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	BTB, NA, NAG, ZN

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5FBA \| pdb_00005fba	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	GOL, NAG, PO4, ZN

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5FBB \| pdb_00005fbb	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	AMP, BTB, CA, ETE, NA, NAG, PO4, ZN

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5FBC \| pdb_00005fbc	Download File View File

S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)).

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	AS, GOL, NAG, ZN

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5FBD \| pdb_00005fbd	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCZ, NAG, PO4, ZN

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5FBF \| pdb_00005fbf	Download File View File

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCM, NA, NAG, ZN

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5FBG \| pdb_00005fbg	Download File View File

S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine.

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCZ, GNG, NAG, PO4, ZN

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5H47 \| pdb_00005h47	Download File View File

Crystal structure of AOL complexed with 2-MeSe-Fuc

Kato, R., Nishikawa, Y., Makyio, H.

(2017) Bioorg Med Chem 25: 1132-1142

Released	2017-01-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Uncharacterized protein (protein)
Unique Ligands	FSW

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5LSV \| pdb_00005lsv	Download File View File

X-ray crystal structure of AA13 LPMO

Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

(2017) Acta Crystallogr D Struct Biol 73: 64-76

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	AoAA13 (protein)
Unique Ligands	NAG, ZN
Unique branched monosaccharides	GLC

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5OR3 \| pdb_00005or3	Download File View File

Crystal structure of Aspergillus oryzae catechol oxidase in met/deoxy-form

Hakulinen, N., Penttinen, L., Rutanen, C., Rouvinen, J.

(2018) PLoS One 13: e0196691-e0196691

Released	2018-05-09
Method	X-RAY DIFFRACTION 1.795 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	catechol oxidase (protein)
Unique Ligands	CU, EDO, FLC, MAN, NAG, PER
Unique branched monosaccharides	BMA, MAN, NAG

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5OR4 \| pdb_00005or4	Download File View File

Crystal structure of Aspergillus oryzae catechol oxidase in deoxy-form

Hakulinen, N., Penttinen, L., Rutanen, C., Rouvinen, J.

(2018) PLoS One 13: e0196691-e0196691

Released	2018-05-09
Method	X-RAY DIFFRACTION 2.445 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	catechol oxidase (protein)
Unique Ligands	CU, MAN, NAG
Unique branched monosaccharides	BMA, NAG

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5T7J \| pdb_00005t7j	Download File View File

X-ray crystal structure of AA13 LPMO

Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

(2017) Acta Crystallogr D Struct Biol 73: 64-76

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	AoAA13 (protein)
Unique Ligands	NAG, ZN

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5T7K \| pdb_00005t7k	Download File View File

X-ray crystal structure of AA13 LPMO

Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

(2017) Acta Crystallogr D Struct Biol 73: 64-76

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	AoAA13 (protein)
Unique Ligands	NAG, ZN

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5T7N \| pdb_00005t7n	Download File View File

X-ray crystal structure of AA13 LPMO

Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

(2017) Acta Crystallogr D Struct Biol 73: 64-76

Released	2017-01-11
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	AoAA13 (protein)
Unique Ligands	NAG, ZN
Unique branched monosaccharides	GLC

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5YOT \| pdb_00005yot	Download File View File

Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose

Matsuzawa, T., Watanabe, M., Nakamichi, Y., Yaoi, K.

(2019) J Struct Biol 205: 84-90

Released	2018-11-07
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Isoprimeverose-producing enzyme (protein)
Unique Ligands	CA, GOL, NAG
Unique branched monosaccharides	NAG

1 to 25 of 49 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

2PS2 | pdb_00002ps2

3C97 | pdb_00003c97

3Q9T | pdb_00003q9t

3SYU | pdb_00003syu

3VX0 | pdb_00003vx0

3VX1 | pdb_00003vx1

3WMT | pdb_00003wmt

4OPB | pdb_00004opb

5EO7 | pdb_00005eo7

5EO8 | pdb_00005eo8

5FB9 | pdb_00005fb9

5FBA | pdb_00005fba

5FBB | pdb_00005fbb

5FBC | pdb_00005fbc

5FBD | pdb_00005fbd

5FBF | pdb_00005fbf

5FBG | pdb_00005fbg

5H47 | pdb_00005h47

5LSV | pdb_00005lsv

5OR3 | pdb_00005or3

5OR4 | pdb_00005or4

5T7J | pdb_00005t7j

5T7K | pdb_00005t7k

5T7N | pdb_00005t7n

5YOT | pdb_00005yot