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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Ferreira de Freitas, R."

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Search Summary

This query matches 114 Structures.

Refinements

Structure Determination Methodology

experimental (114)

Scientific Name of Source Organism

	Mus musculus (24)
	Streptomyces rubiginosus (24)
	Homo sapiens (19)
	Trichoderma reesei (13)
	Escherichia coli K-12 (7)
	synthetic construct (7)
	Trichoderma reesei RUT C-30 (5)
	Severe acute respiratory syndrome coronavirus 2 (4)
	Cryphonectria parasitica (3)
	Human immunodeficiency virus 1 (3)

More...

Taxonomy

	Eukaryota (59)
	Bacteria (39)
	Riboviria (8)
	other sequences (7)
	Archaea (3)

Experimental Method

	X-RAY DIFFRACTION (106)
	NEUTRON DIFFRACTION (45)

Polymer Entity Type

	Protein (110)
	DNA (4)

Refinement Resolution (Å)

	0.5 - 1.0 (4)
	1.0 - 1.5 (13)
	1.5 - 2.0 (66)
	2.0 - 2.5 (45)
	2.5 - 3.0 (5)

Release Date

	1995 - 1999 (1)
	2005 - 2009 (13)
	2010 - 2014 (55)
	2015 - 2019 (32)
	2020 - 2024 (13)

Enzyme Classification Name

	Hydrolases (35)
	Transferases (28)
	Isomerases (24)
	Oxidoreductases (9)
	Lyases (4)

Symmetry Type

	Asymmetric (69)
	Dihedral (27)
	Cyclic (14)

SCOP Classification

	All beta proteins (38)
	Alpha and beta proteins (a/b) (36)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (4)
	Artifacts (2)
	Small proteins (2)

AllSelected

1 to 25 of 114 Structures

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1LZN \| pdb_00001lzn	Download File View File

NEUTRON STRUCTURE OF HEN EGG-WHITE LYSOZYME

Bon, C.I., Lehmann, M.S., Wilkinson, C.

(1999) Acta Crystallogr D Biol Crystallogr 55: 978-987

Released	1999-04-01
Method	NEUTRON DIFFRACTION 1.7 Å
Organisms	Gallus gallus
Macromolecule	PROTEIN (LYSOZYME) (protein)
Unique Ligands	NA, NO3

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2GLK \| pdb_00002glk	Download File View File

High-resolution study of D-Xylose isomerase, 0.94A resolution.

Katz, A.K., Carrell, H.L., Hanson, B.L., Harp, J.M., Glusker, J.P., Bunick, G.J.

(2006) Proc Natl Acad Sci U S A 103: 8342-8347

Released	2006-05-16
Method	X-RAY DIFFRACTION 0.94 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GOL, MN

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2GUB \| pdb_00002gub	Download File View File

Crystal Structure of Metal Free D-Xylose Isomerase.

Carrell, H.L., Katz, A.K., Glusker, J.P.

(2006) Proc Natl Acad Sci U S A 103: 8342-8347

Released	2006-05-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)

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2GVE \| pdb_00002gve	Download File View File

Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase

Katz, A.K., Li, X., Carrell, H.L., Hanson, B.L., Langan, P., Coates, L., Schoenborn, B.P., Glusker, J.P., Bunick, G.J.

(2006) Proc Natl Acad Sci U S A 103: 8342-8347

Released	2006-05-16
Method	NEUTRON DIFFRACTION 2.2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CO

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2JJI \| pdb_00002jji	Download File View File

Endothiapepsin in complex with a gem-diol inhibitor.

Coates, L., Tuan, H.-F., Tomanicek, S.J., Kovalevsky, A., Mustyakimov, M., Erskine, P., Cooper, J.

(2008) J Am Chem Soc 130: 7235

Released	2008-05-27
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Cryphonectria parasitica
Macromolecule	ENDOTHIAPEPSIN (protein)
Unique Ligands	0QS, SO4

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2JJJ \| pdb_00002jjj	Download File View File

Endothiapepsin in complex with a gem-diol inhibitor.

Coates, L., Tuan, H.-F., Tomanicek, S.J., Kovalevsky, A., Mustyakimov, M., Erskine, P., Cooper, J.

(2008) J Am Chem Soc 130: 7235

Released	2008-05-27
Method	X-RAY DIFFRACTION 1 Å
Organisms	Cryphonectria parasitica
Macromolecule	ENDOTHIAPEPSIN (protein)
Unique Ligands	0QS, SO4

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2PKY \| pdb_00002pky	Download File View File

The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase

Liu, X., Hanson, L., Langan, P., Viola, R.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1000-1008

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Xanthobacter autotrophicus
Macromolecule	Haloalkane dehalogenase (protein)

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2QWS \| pdb_00002qws	Download File View File

Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)

Fisher, S.Z., Langan, P.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1178-1184

Released	2008-03-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Halorhodospira halophila
Macromolecule	Photoactive yellow protein (protein)
Unique Ligands	HC4

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2VS2 \| pdb_00002vs2	Download File View File

Neutron diffraction structure of endothiapepsin in complex with a gem- diol inhibitor.

Coates, L., Tuan, H.-F., Tomanicek, S., Kovalevsky, A., Mustyakimov, M., Erskine, P., Cooper, J.

(2008) J Am Chem Soc 130: 7235

Released	2008-05-27
Method	NEUTRON DIFFRACTION 2 Å
Organisms	Cryphonectria parasitica
Macromolecule	ENDOTHIAPEPSIN (protein)
Unique Ligands	0QS

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2YXP \| pdb_00002yxp	Download File View File

The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase

Liu, X., Hanson, L., Langan, P., Viola, R.E.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1000-1008

Released	2007-09-04
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Xanthobacter autotrophicus
Macromolecule	Haloalkane dehalogenase (protein)

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3BYC \| pdb_00003byc	Download File View File

Joint neutron and X-ray structure of diisopropyl fluorophosphatase. Deuterium occupancies are 1-Q, where Q is occupancy of H

Blum, M.-M., Mustyakimov, M., Ruterjans, H., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

(2009) Proc Natl Acad Sci U S A 106: 713-718

Released	2009-01-27
Method	X-RAY DIFFRACTION 2.2 Å NEUTRON DIFFRACTION 2.2 Å
Organisms	Loligo vulgaris
Macromolecule	Diisopropyl-fluorophosphatase (protein)
Unique Ligands	CA

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3CWH \| pdb_00003cwh	Download File View File

D-xylose Isomerase in complex with linear product, per-deuterated xylulose

Kovalevsky, A.Y., Langan, P., Glusker, J.P.

(2008) Biochemistry 47: 7595-7597

Released	2008-08-05
Method	NEUTRON DIFFRACTION 2.2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, OH, XUL

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3DAT \| pdb_00003dat	Download File View File

Crystal structure of the ternary MTX NADPH complex of Bacillus anthracis dihydrofolate reductase

Bennett, B.C., Dealwis, C.G.

(2009) J Struct Biol 166: 162-171

Released	2009-04-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bacillus anthracis str. Sterne
Macromolecule	Dihydrofolate reductase (protein)
Unique Ligands	MTX, NDP

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3DAU \| pdb_00003dau	Download File View File

Crystal structure of the ternary MTX NADPH complex of Escherichia coli dihydrofolate reductase

Bennett, B.C., Dealwis, C.G.

(2009) J Struct Biol 166: 162-171

Released	2009-04-14
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli K-12
Macromolecule	Dihydrofolate reductase (protein)
Unique Ligands	MTX, NDP

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3KBJ \| pdb_00003kbj	Download File View File

Room temperature X-ray structure of apo-D-Xylose Isomerase

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2010-09-29
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)

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3KBM \| pdb_00003kbm	Download File View File

Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD, GLC

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3KBN \| pdb_00003kbn	Download File View File

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.53 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GLO, NI

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3KBS \| pdb_00003kbs	Download File View File

Room Temperature X-ray structure of D-Xylose Isomerase in complex with 2Cd(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD

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3KBV \| pdb_00003kbv	Download File View File

Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	NI

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3KBW \| pdb_00003kbw	Download File View File

Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors

Kovalevsky, A.Y., Hanson, L., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	MG, NI

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3KCJ \| pdb_00003kcj	Download File View File

Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)

Kovalevsky, A.Y., Langan, P.

(2011) Angew Chem Int Ed Engl 50: 7520-7523

Released	2010-09-29
Method	NEUTRON DIFFRACTION 1.8 Å X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)

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3KCL \| pdb_00003kcl	Download File View File

Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

Kovalevsky, A.Y., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	NEUTRON DIFFRACTION 2 Å X-RAY DIFFRACTION 2 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	CD, GLC

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3KCO \| pdb_00003kco	Download File View File

Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)

Kovalevsky, A.Y., Langan, P.

(2010) Structure 18: 688-699

Released	2010-06-16
Method	NEUTRON DIFFRACTION 1.8 Å X-RAY DIFFRACTION 1.53 Å
Organisms	Streptomyces rubiginosus
Macromolecule	Xylose isomerase (protein)
Unique Ligands	GLO, NI

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3KGG \| pdb_00003kgg	Download File View File

X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): Perdeuteration of proteins for neutron diffraction

Blum, M.-M., Tomanicek, S.J., John, H., Hanson, B.L., terjans, H.R., Schoenborn, B.P., Langan, P., Chen, J.C.-H.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 379-385

Released	2010-04-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Loligo vulgaris
Macromolecule	Diisopropyl-fluorophosphatase (protein)
Unique Ligands	CA

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3KMF \| pdb_00003kmf	Download File View File

Room Temperature Time-of-Flight Neutron Diffraction Study of Deoxy Human Normal Adult Hemoglobin

Kovalevsky, A.Y., Morimoto, Y., Chatake, T.

(2010) J Mol Biology 398: 276-291

Released	2010-04-21
Method	NEUTRON DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Hemoglobin subunit alpha (protein) Hemoglobin subunit beta (protein)
Unique Ligands	HEM

1 to 25 of 114 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

1LZN | pdb_00001lzn

2GLK | pdb_00002glk

2GUB | pdb_00002gub

2GVE | pdb_00002gve

2JJI | pdb_00002jji

2JJJ | pdb_00002jjj

2PKY | pdb_00002pky

2QWS | pdb_00002qws

2VS2 | pdb_00002vs2

2YXP | pdb_00002yxp

3BYC | pdb_00003byc

3CWH | pdb_00003cwh

3DAT | pdb_00003dat

3DAU | pdb_00003dau

3KBJ | pdb_00003kbj

3KBM | pdb_00003kbm

3KBN | pdb_00003kbn

3KBS | pdb_00003kbs

3KBV | pdb_00003kbv

3KBW | pdb_00003kbw

3KCJ | pdb_00003kcj

3KCL | pdb_00003kcl

3KCO | pdb_00003kco

3KGG | pdb_00003kgg

3KMF | pdb_00003kmf