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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Paracoccus denitrificans"

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Search Summary

This query matches 143 Structures.

Refinements

Structure Determination Methodology

experimental (143)

Scientific Name of Source Organism

	Paracoccus denitrificans (91)
	Paracoccus denitrificans PD1222 (61)
	Mus musculus (4)
	Paracoccus pantotrophus (1)

Taxonomy

	Bacteria (143)
	Eukaryota (4)

Experimental Method

	X-RAY DIFFRACTION (132)
	ELECTRON MICROSCOPY (6)
	SOLUTION NMR (5)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

Protein (143)

Refinement Resolution (Å)

	0.5 - 1.0 (7)
	1.0 - 1.5 (19)
	1.5 - 2.0 (35)
	2.0 - 2.5 (55)
	2.5 - 3.0 (18)
	3.0 - 3.5 (3)
	3.5 - 4.0 (1)

Release Date

	1975 - 1979 (1)
	1990 - 1994 (6)
	1995 - 1999 (18)
	2000 - 2004 (20)
	2005 - 2009 (29)
	2010 - 2014 (43)
	2015 - 2019 (12)
	2020 - 2024 (11)
	2025 - 2029 (3)

Enzyme Classification Name

	Oxidoreductases (53)
	Translocases (12)
	Transferases (14)
	Lyases (3)
	Isomerases (4)
	Hydrolases (2)

Membrane Protein Annotation

	PDBTM (12)
	MemProtMD (10)
	OPM (9)
	mpstruc (3)

Symmetry Type

	Asymmetric (69)
	Cyclic (66)
	Dihedral (14)

SCOP Classification

	All beta proteins (64)
	Small proteins (38)
	Alpha and beta proteins (a/b) (24)
	All alpha proteins (19)
	Artifacts (18)
	Alpha and beta proteins (a+b) (7)
	Membrane and cell surface proteins and peptides (4)

AllSelected

1 to 25 of 143 Structures

Page 1 of 6

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155C \| pdb_0000155c	Download File View File

THE STRUCTURE OF PARACOCCUS DENITRIFICANS CYTOCHROME C550

Timkovich, R.

(1976) J Biological Chem 251: 4033-4046

Released	1976-08-20
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Paracoccus denitrificans
Macromolecule	CYTOCHROME C550 (protein)
Unique Ligands	HEM

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1AAC \| pdb_00001aac	Download File View File

AMICYANIN OXIDIZED, 1.31 ANGSTROMS

Cunane, L.M., Chen, Z.-W., Durley, R.C.E., Mathews, F.S.

(1996) Acta Crystallogr D Biol Crystallogr 52: 676-686

Released	1996-03-08
Method	X-RAY DIFFRACTION 1.31 Å
Organisms	Paracoccus denitrificans
Macromolecule	AMICYANIN (protein)
Unique Ligands	CU

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1AAJ \| pdb_00001aaj	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF AMICYANIN AND APOAMICYANIN FROM PARACOCCUS DENITRIFICANS AT 2.0 ANGSTROMS AND 1.8 ANGSTROMS RESOLUTION

Durley, R.C.E., Chen, L., Lim, L.W., Mathews, F.S.

(1993) Protein Sci 2: 739-752

Released	1993-10-31
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Paracoccus denitrificans
Macromolecule	AMICYANIN (protein)

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1AAN \| pdb_00001aan	Download File View File

CRYSTAL STRUCTURE ANALYSIS OF AMICYANIN AND APOAMICYANIN FROM PARACOCCUS DENITRIFICANS AT 2.0 ANGSTROMS AND 1.8 ANGSTROMS RESOLUTION

Chen, L., Durley, R.C.E., Lim, L.W., Mathews, F.S.

(1993) Protein Sci 2: 739-752

Released	1993-10-31
Method	X-RAY DIFFRACTION 2 Å
Organisms	Paracoccus denitrificans
Macromolecule	AMICYANIN (protein)
Unique Ligands	CU

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1AR1 \| pdb_00001ar1	Download File View File

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

Ostermeier, C., Harrenga, A., Ermler, U., Michel, H.

(1997) Proc Natl Acad Sci U S A 94: 10547-10553

Released	1998-02-11
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus Paracoccus denitrificans
Macromolecule	ANTIBODY FV FRAGMENT (protein) CYTOCHROME C OXIDASE (protein)
Unique Ligands	CA, CU, HEA, LDA, MG

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1AY4 \| pdb_00001ay4	Download File View File

AROMATIC AMINO ACID AMINOTRANSFERASE WITHOUT SUBSTRATE

Okamoto, A., Hirotsu, K., Kagamiyama, H.

(1998) J Mol Biology 280: 443-461

Released	1998-10-14
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Paracoccus denitrificans
Macromolecule	AROMATIC AMINO ACID AMINOTRANSFERASE (protein)
Unique Ligands	PLP

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1AY5 \| pdb_00001ay5	Download File View File

AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH MALEATE

Okamoto, A., Hirotsu, K., Kagamiyama, H.

(1998) J Mol Biology 280: 443-461

Released	1998-10-14
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Paracoccus denitrificans
Macromolecule	AROMATIC AMINO ACID AMINOTRANSFERASE (protein)
Unique Ligands	MAE, PLP

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1AY8 \| pdb_00001ay8	Download File View File

AROMATIC AMINO ACID AMINOTRANSFERASE COMPLEX WITH 3-PHENYLPROPIONATE

Okamoto, A., Hirotsu, K., Kagamiyama, H.

(1998) J Mol Biology 280: 443-461

Released	1998-10-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Paracoccus denitrificans
Macromolecule	AROMATIC AMINO ACID AMINOTRANSFERASE (protein)
Unique Ligands	HCI, PLP

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1BXA \| pdb_00001bxa	Download File View File

AMICYANIN REDUCED, PH 4.4, 1.3 ANGSTROMS

Cunane, L.M., Chen, Z.W., Durley, R.C.E., Mathews, F.S.

(1998) Biochemistry 37: 17128-17136

Released	1998-10-07
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Paracoccus denitrificans
Macromolecule	PROTEIN (AMICYANIN) (protein)
Unique Ligands	CU1

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1C7M \| pdb_00001c7m	Download File View File

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

Pristovsek, P., Luecke, C., Reincke, B., Ludwig, B., Rueterjans, H.

(2000) Eur J Biochem 267: 4205-4212

Released	2000-07-19
Method	SOLUTION NMR
Organisms	Paracoccus denitrificans
Macromolecule	PROTEIN (CYTOCHROME C552) (protein)
Unique Ligands	HEC

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1COT \| pdb_00001cot	Download File View File

X-RAY STRUCTURE OF THE CYTOCHROME C2 ISOLATED FROM PARACOCCUS DENITRIFICANS REFINED TO 1.7 ANGSTROMS RESOLUTION

Benning, M.M., Meyer, T.E., Holden, H.M.

(1994) Arch Biochem Biophys 310: 460-466

Released	1994-09-30
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Paracoccus denitrificans
Macromolecule	CYTOCHROME C2 (protein)
Unique Ligands	HEC

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1E2R \| pdb_00001e2r	Download File View File

CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND

Fulop, V.

(2000) J Biological Chem 275: 25089

Released	2000-05-30
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Paracoccus denitrificans
Macromolecule	NITRITE REDUCTASE (protein)
Unique Ligands	CYN, DHE, GOL, HEC

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1EFP \| pdb_00001efp	Download File View File

ELECTRON TRANSFER FLAVOPROTEIN (ETF) FROM PARACOCCUS DENITRIFICANS

Roberts, D.L., Salazar, D., Fulmer, J.P., Frerman, F.E., Kim, J.J.-P.

(1999) Biochemistry 38: 1977-1989

Released	1999-08-09
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Paracoccus denitrificans
Macromolecule	PROTEIN (ELECTRON TRANSFER FLAVOPROTEIN) (protein)
Unique Ligands	AMP, FAD

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1FWX \| pdb_00001fwx	Download File View File

CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS

Brown, K., Djinovic-Carugo, K., Haltia, T., Cabrito, I., Saraste, M., Moura, J.J., Moura, I., Tegoni, M., Cambillau, C.

(2000) J Biological Chem 275: 41133-41136

Released	2001-09-25
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Paracoccus denitrificans
Macromolecule	NITROUS OXIDE REDUCTASE (protein)
Unique Ligands	CA, CL, CUA, CUZ

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1I6D \| pdb_00001i6d	Download File View File

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

Reincke, B., Perez, C., Pristovsek, P., Luecke, C., Ludwig, C., Loehr, F., Rogov, V.V., Ludwig, B., Rueterjans, H.

(2001) Biochemistry 40: 12312-12320

Released	2001-10-17
Method	SOLUTION NMR
Organisms	Paracoccus denitrificans
Macromolecule	CYTOCHROME C552 (protein)
Unique Ligands	HEC

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1I6E \| pdb_00001i6e	Download File View File

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE OXIDIZED STATE

Reincke, B., Perez, C., Pristovsek, P., Luecke, C., Ludwig, C., Loehr, F., Rogov, V.V., Ludwig, B., Rueterjans, H.

(2001) Biochemistry 40: 12312-12320

Released	2001-10-17
Method	SOLUTION NMR
Organisms	Paracoccus denitrificans
Macromolecule	CYTOCHROME C552 (protein)
Unique Ligands	HEC

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1IOK \| pdb_00001iok	Download File View File

CRYSTAL STRUCTURE OF CHAPERONIN-60 FROM PARACOCCUS DENITRIFICANS

Fukami, T.A., Yohda, M., Taguchi, H., Yoshida, M., Miki, K.

(2001) J Mol Biology 312: 501-509

Released	2001-10-03
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Paracoccus denitrificans
Macromolecule	CHAPERONIN 60 (protein)

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1JJU \| pdb_00001jju	Download File View File

Structure of a Quinohemoprotein Amine Dehydrogenase with a Unique Redox Cofactor and Highly Unusual Crosslinking

Datta, S., Mori, Y., Takagi, K., Kawaguchi, K., Chen, Z.-W., Kano, K., Ikeda, T., Okajima, T., Kuroda, S., Tanizawa, K., Mathews, F.S.

(2001) Proc Natl Acad Sci U S A 98: 14268-14273

Released	2001-12-12
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Paracoccus denitrificans
Macromolecule	QUINOHEMOPROTEIN AMINE DEHYDROGENASE (protein)
Unique Ligands	HEM, NA, TBU

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1LRW \| pdb_00001lrw	Download File View File

Crystal structure of methanol dehydrogenase from P. denitrificans

Xia, Z.-X., Dai, W.-W., He, Y.-N., White, S.A., Mathews, F.S., Davidson, V.L.

(2003) J Biol Inorg Chem 8: 843-854

Released	2003-08-12
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Paracoccus denitrificans
Macromolecule	methanol dehydrogenase subunit 1 (protein) methanol dehydrogenase subunit 2 (protein)
Unique Ligands	CA, PQQ

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1MDA \| pdb_00001mda	Download File View File

CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN

Chen, L., Durley, R., Mathews, F.S.

(1992) Biochemistry 31: 4959-4964

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Paracoccus denitrificans
Macromolecule	AMICYANIN (protein) METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT) (protein) METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT) (protein)
Unique Ligands	CU

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1MG2 \| pdb_00001mg2	Download File View File

MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN

Sun, D., Chen, Z.W., Mathews, F.S., Davidson, V.L.

(2002) Biochemistry 41: 13926-13933

Released	2002-12-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Paracoccus denitrificans
Macromolecule	Amicyanin (protein) CYTOCHROME C-L (protein) Methylamine dehydrogenase, heavy chain (protein) Methylamine dehydrogenase, light chain (protein)
Unique Ligands	CU, HEC, NA, PO4

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1MG3 \| pdb_00001mg3	Download File View File

MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN

Sun, D., Chen, Z.W., Mathews, F.S., Davidson, V.L.

(2002) Biochemistry 41: 13926-13933

Released	2002-12-11
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Paracoccus denitrificans
Macromolecule	Amicyanin (protein) CYTOCHROME C-L (protein) Methylamine dehydrogenase, heavy chain (protein) Methylamine dehydrogenase, light chain (protein)
Unique Ligands	CU, HEC, NA, PO4

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1PBY \| pdb_00001pby	Download File View File

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

Datta, S., Ikeda, T., Kano, K., Mathews, F.S.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1551-1556

Released	2003-09-02
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Paracoccus denitrificans
Macromolecule	quinohemoprotein amine dehydrogenase 40 kDa subunit (protein) quinohemoprotein amine dehydrogenase 60 kDa subunit (protein) quinohemoprotein amine dehydrogenase 9 kDa subunit (protein)
Unique Ligands	HEC, TBU