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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Fernandez, D."

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Search Summary

This query matches 49 Structures.

Refinements

Structure Determination Methodology

experimental (49)

Scientific Name of Source Organism

	Severe acute respiratory syndrome coronavirus 2 (15)
	Homo sapiens (11)
	Aspergillus fumigatus Af293 (5)
	Bos taurus (4)
	Gallus gallus (2)
	HIV-1 M:B_HXB2R (2)
	Mus musculus (2)
	Xanthomonas citri (2)
	synthetic construct (2)
	Akkermansia muciniphila ATCC BAA-835 (1)

More...

Taxonomy

	Eukaryota (27)
	Riboviria (17)
	Bacteria (4)
	other sequences (2)

Experimental Method

X-RAY DIFFRACTION (49)

Polymer Entity Type

	Protein (49)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (27)
	2.0 - 2.5 (12)
	2.5 - 3.0 (3)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (5)
	2010 - 2014 (4)
	2015 - 2019 (5)
	2020 - 2024 (35)

Enzyme Classification Name

	Hydrolases (32)
	Oxidoreductases (3)
	Transferases (1)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (21)
	Cyclic (27)
	Dihedral (1)

SCOP Classification

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

AllSelected

1 to 25 of 49 Structures

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2PCU \| pdb_00002pcu	Download File View File

Human carboxypeptidase A4 in complex with a cleaved hexapeptide.

Bayes, A., Fernandez, D., Sola, M., Marrero, A., Garcia-Pique, S., Aviles, F.X., Vendrell, J., Gomis-Ruth, F.X.

(2007) Biochemistry 46: 6921-6930

Released	2007-04-17
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Carboxypeptidase A4 (protein) peptide (protein)
Unique Ligands	ASP, GOL, NAG, SCN, ZN

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2V77 \| pdb_00002v77	Download File View File

Crystal Structure of Human Carboxypeptidase A1

Pallares, I., Fernandez, D., Comellas-Bigler, M., Fernandez-Recio, J., Ventura, S., Aviles, F.X., Vendrell, J.

(2008) Acta Crystallogr D Biol Crystallogr D64: 784-791

Released	2008-07-01
Method	X-RAY DIFFRACTION 1.603 Å
Organisms	Homo sapiens
Macromolecule	CARBOXYPEPTIDASE A1 (protein)
Unique Ligands	EPE, PAY, ZN

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3DWC \| pdb_00003dwc	Download File View File

Trypanosoma Cruzi Metallocarboxypeptidase 1

Niemirowicz, G., Fernandez, D., Sola, M., Cazzulo, J.J., Aviles, F.X., Gomis-Ruth, F.X.

(2008) Mol Microbiol 70: 853-866

Released	2008-09-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Trypanosoma cruzi
Macromolecule	Metallocarboxypeptidase (protein)
Unique Ligands	ALA, CO, GLY, GOL, SO4

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3GLJ \| pdb_00003glj	Download File View File

A polymorph of carboxypeptidase B zymogen structure

Fernandez, D.

(2009) Biopolymers

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Sus scrofa
Macromolecule	Carboxypeptidase B (protein)
Unique Ligands	GOL, ZN

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3HLP \| pdb_00003hlp	Download File View File

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

Fernandez, D.

To be published

Released	2010-06-02
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Bos taurus
Macromolecule	Carboxypeptidase A1 (Pancreatic) (protein)
Unique Ligands	MPD, MRD, ZN

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3HUV \| pdb_00003huv	Download File View File

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

Fernandez, D., Boix, E., Aviles, F.X., Vendrell, J.

To be published

Released	2010-06-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Carboxypeptidase A1 (Pancreatic) (protein)
Unique Ligands	ZN

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3I1U \| pdb_00003i1u	Download File View File

Carboxypeptidase A Inhibited by a Thiirane Mechanism-Based inactivator

Fernandez, D.

(2010) Chem Biol Drug Des 75: 29-34

Released	2009-11-17
Method	X-RAY DIFFRACTION 1.391 Å
Organisms	Bos taurus
Macromolecule	Carboxypeptidase A1 (Pancreatic) (protein)
Unique Ligands	BTW, GOL, ZN

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3KGQ \| pdb_00003kgq	Download File View File

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

Fernandez, D., Boix, E., Pallares, I., Aviles, F.X., Vendrell, J.

(2011) Enzyme Res 2011: 128676-128676

Released	2010-10-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Bos taurus
Macromolecule	Carboxypeptidase A1 (protein)
Unique Ligands	ACN, CIT, FMT, GOL, NA, ZN

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4K90 \| pdb_00004k90	Download File View File

Extracellular metalloproteinase from Aspergillus

Fernandez, D., Russi, S., Vendrell, J., Monod, M., Pallares, I.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1946-1957

Released	2013-10-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus fumigatus Af293
Macromolecule	Extracellular metalloproteinase mep (protein)
Unique Ligands	BO3, CA, GOL, MLA, ZN
Unique branched monosaccharides	BMA, NAG

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5A52 \| pdb_00005a52	Download File View File

The crystal structure of Arabidopsis thaliana CAR1 in complex with one calcium ion

Fernandez, D., Marquez, J.A.

(2016) Proc Natl Acad Sci U S A 113: E396

Released	2016-03-02
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Arabidopsis thaliana
Macromolecule	CALCIUM-DEPENDENT LIPID-BINDING DOMAIN-CONTAINING PROTEIN (protein)
Unique Ligands	CA, GOL, SO4

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5OM9 \| pdb_00005om9	Download File View File

Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with a thiirane mechanism-based inhibitor

Gallego, P., Granados, C., Fernandez, D., Pallares, I., Covaleda, G., Aviles, F.X., Vendrell, J., Reverter, D.

(2017) ACS Med Chem Lett 8: 1122-1127

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Carboxypeptidase A1 (protein)
Unique Ligands	O2S, ZN

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6CFF \| pdb_00006cff	Download File View File

Stimulator of Interferon Genes Human

Fernandez, D., Li, L., Ergun, S.L.

(2019) Cell 178: 290-301.e10

Released	2019-03-13
Method	X-RAY DIFFRACTION 2.396 Å
Organisms	Homo sapiens
Macromolecule	Stimulator of interferon genes protein (protein)
Unique Ligands	2BA

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6CY7 \| pdb_00006cy7	Download File View File

Human Stimulator of Interferon Genes

Fernandez, D., Li, L., Ergun, S.L.

(2019) Cell 178: 290-301.e10

Released	2019-03-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Stimulator of interferon genes protein (protein)
Unique Ligands	2BA, GOL, IMD

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6DNK \| pdb_00006dnk	Download File View File

Human Stimulator of Interferon Genes

Fernandez, D., Li, L., Ergun, S.L.

(2019) Cell 178: 290-301.e10

Released	2019-03-13
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	Stimulator of interferon genes protein (protein)
Unique Ligands	1SY

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6NQT \| pdb_00006nqt	Download File View File

GalNac-T2 soaked with UDP-sugar

Fernandez, D., Bertozzi, C.R., Schumann, B., Agbay, A.

(2020) Mol Cell 78: 824-834.e15

Released	2020-01-29
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Homo sapiens
Macromolecule	Polypeptide N-acetylgalactosaminyltransferase 2 (protein)
Unique Ligands	LR7, MN

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6W7P \| pdb_00006w7p	Download File View File

Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment

Fernandez, D., Russi, S.

(2020) NPJ Microgravity 6: 12-12

Released	2020-04-29
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme (protein)
Unique Ligands	CL, NA

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6W8E \| pdb_00006w8e	Download File View File

Crystal Structure Analysis of Space-grown Lysozyme

Fernandez, D., Russi, S.

(2020) NPJ Microgravity 6: 12-12

Released	2020-04-29
Method	X-RAY DIFFRACTION 2.68 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme (protein)
Unique Ligands	CL

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6XKD \| pdb_00006xkd	Download File View File

Structure of ligand-bound mouse cGAMP hydrolase ENPP1

Fernandez, D., Li, L.

(2020) Cell Chem Biol 27: 1347-1358.e5

Released	2021-06-02
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Mus musculus
Macromolecule	Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 (protein)
Unique Ligands	CA, CL, IJE, NAG, ZN
Unique branched monosaccharides	BMA, MAN, NAG

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7MJC \| pdb_00007mjc	Download File View File

Crystal Structure Analysis of ALDH1B1

Fernandez, D., Chen, J.K.

(2022) Nat Chem Biol

Released	2022-06-08
Method	X-RAY DIFFRACTION 2.68 Å
Organisms	Homo sapiens
Macromolecule	Aldehyde dehydrogenase X, mitochondrial (protein)
Unique Ligands	NA, NAD

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7MJD \| pdb_00007mjd	Download File View File

Crystal Structure Analysis of ALDH1B1

Fernandez, D., Chen, J.K.

(2022) Nat Chem Biol

Released	2022-06-08
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Homo sapiens
Macromolecule	Aldehyde dehydrogenase X, mitochondrial (protein)
Unique Ligands	1PE, GOL, NA, NAD, ZGG

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7MW8 \| pdb_00007mw8	Download File View File

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

Fernandez, D., Li, L., Brown, J.A.

(2022) Proc Natl Acad Sci U S A 119: e2119189119-e2119189119

Released	2022-05-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Xanthomonas citri synthetic construct
Macromolecule	Phosphodiesterase-nucleotide pyrophosphatase (protein) pApG (nucleic acid)
Unique Ligands	ZN

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7N1S \| pdb_00007n1s	Download File View File

Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase

Fernandez, D., Li, L., Brown, J.A., Carozza, J.A.

(2022) Proc Natl Acad Sci U S A 119: e2119189119-e2119189119

Released	2022-06-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Xanthomonas citri
Macromolecule	Phosphodiesterase-nucleotide pyrophosphatase (protein)
Unique Ligands	PG4, ZN

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7RAD \| pdb_00007rad	Download File View File

Crystal Structure Analysis of ALDH1B1

Fernandez, D., Chen, J.K.

(2022) Nat Chem Biol

Released	2022-06-08
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Aldehyde dehydrogenase X, mitochondrial (protein)
Unique Ligands	EDO, NA, NAD, ZGJ

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7SCI \| pdb_00007sci	Download File View File

AM0627 metallopeptidase from Akkermansia muciniphila

Fernandez, D., Bertozzi, C.R., Shon, D.J.

(2022) J Biological Chem 298: 101917-101917

Released	2022-04-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Akkermansia muciniphila ATCC BAA-835
Macromolecule	Peptidase M60 domain-containing protein (protein)
Unique Ligands	CL, FMT, PGE, ZN

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7SET \| pdb_00007set	Download File View File

SARS-CoV-2 Main Protease (Mpro) in Complex with ML1000

Westberg, M., Fernandez, D., Lin, M.Z.

(2024) Sci Transl Med 16: eadi0979-eadi0979

Released	2022-10-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Severe acute respiratory syndrome coronavirus 2
Macromolecule	3C-like proteinase (protein)
Unique Ligands	CL, I70

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

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2PCU | pdb_00002pcu

2V77 | pdb_00002v77

3DWC | pdb_00003dwc

3GLJ | pdb_00003glj

3HLP | pdb_00003hlp

3HUV | pdb_00003huv

3I1U | pdb_00003i1u

3KGQ | pdb_00003kgq

4K90 | pdb_00004k90

5A52 | pdb_00005a52

5OM9 | pdb_00005om9

6CFF | pdb_00006cff

6CY7 | pdb_00006cy7

6DNK | pdb_00006dnk

6NQT | pdb_00006nqt

6W7P | pdb_00006w7p

6W8E | pdb_00006w8e

6XKD | pdb_00006xkd

7MJC | pdb_00007mjc

7MJD | pdb_00007mjd

7MW8 | pdb_00007mw8

7N1S | pdb_00007n1s

7RAD | pdb_00007rad

7SCI | pdb_00007sci

7SET | pdb_00007set