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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Ornelas, E."

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Search Summary

This query matches 686 Structures.

Refinements

Structure Determination Methodology

experimental (686)

Scientific Name of Source Organism

	Homo sapiens (224)
	Severe acute respiratory syndrome coronavirus 2 (117)
	Mus musculus (39)
	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (31)
	Bacteroides thetaiotaomicron VPI-5482 (22)
	synthetic construct (20)
	Human immunodeficiency virus 1 (14)
	Klebsiella pneumoniae (14)
	Pseudomonas aeruginosa PAO1 (13)
	Bacteroides thetaiotaomicron (12)

More...

Taxonomy

	Eukaryota (315)
	Bacteria (263)
	Riboviria (162)
	other sequences (22)
	Archaea (13)
	Varidnaviria (7)
	Duplodnaviria (6)
	unclassified sequences (2)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (418)
	ELECTRON MICROSCOPY (261)
	SOLUTION NMR (7)

Polymer Entity Type

	Protein (684)
	RNA (40)
	DNA (23)

Refinement Resolution (Å)

	0.5 - 1.0 (6)
	1.0 - 1.5 (28)
	1.5 - 2.0 (119)
	2.0 - 2.5 (163)
	2.5 - 3.0 (127)
	3.0 - 3.5 (120)
	3.5 - 4.0 (60)
	4.0 - 4.5 (24)
	> 4.5 (32)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (6)
	2005 - 2009 (26)
	2010 - 2014 (63)
	2015 - 2019 (161)
	2020 - 2024 (400)
	2025 - 2029 (28)

Enzyme Classification Name

	Hydrolases (182)
	Transferases (86)
	Isomerases (18)
	Ligases (14)
	Oxidoreductases (14)
	Lyases (11)
	Translocases (4)

Membrane Protein Annotation

	PDBTM (86)
	mpstruc (50)
	OPM (51)
	MemProtMD (53)

Symmetry Type

	Asymmetric (413)
	Cyclic (246)
	Dihedral (23)
	Helical (9)
	Icosahedral (3)
	Octahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (45)
	All alpha proteins (27)
	Alpha and beta proteins (a/b) (27)
	All beta proteins (21)
	Artifacts (9)
	Coiled coil proteins (2)
	Membrane and cell surface proteins and peptides (5)
	Small proteins (3)
	Peptides (2)

AllSelected

1 to 25 of 686 Structures

Page 1 of 28

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1EGT \| pdb_00001egt	Download File View File

THROMBIN-BOUND STRUCTURE OF AN EGF SUBDOMAIN FROM HUMAN THROMBOMODULIN DETERMINED BY TRANSFERRED NUCLEAR OVERHAUSER EFFECTS

Ni, F.

(1994) Biochemistry 33: 13553-13560

Released	1995-11-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	THROMBOMODULIN (protein)

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1F2S \| pdb_00001f2s	Download File View File

CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN BOVINE BETA-TRYPSIN AND MCTI-A, A TRYPSIN INHIBITOR OF SQUASH FAMILY AT 1.8 A RESOLUTION

Zhu, Y., Huang, Q., Qian, M., Jia, Y., Tang, Y.

(1999) J Protein Chem 18: 505-509

Released	2000-06-05
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Bos taurus Momordica charantia
Macromolecule	TRYPSIN (protein) TRYPSIN INHIBITOR A (protein)
Unique Ligands	CA

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1G9I \| pdb_00001g9i	Download File View File

CRYSTAL STRUCTURE OF BETA-TRYSIN COMPLEX IN CYCLOHEXANE

Zhu, G., Huang, Q., Zhu, Y., Li, Y., Chi, C., Tang, Y.

(2001) Biochim Biophys Acta 1546: 98-106

Released	2000-12-06
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus Vigna radiata var. radiata
Macromolecule	BOWMAN-BIRK TYPE TRYPSIN INHIBITOR (protein) TRYPSINOGEN, CATIONIC (protein)
Unique Ligands	CA, SO4

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1JOY \| pdb_00001joy	Download File View File

SOLUTION STRUCTURE OF THE HOMODIMERIC DOMAIN OF ENVZ FROM ESCHERICHIA COLI BY MULTI-DIMENSIONAL NMR.

Tomomori, C., Tanaka, T., Dutta, R., Park, H., Saha, S.K., Zhu, Y., Ishima, R., Liu, D., Tong, K.I., Kurokawa, H., Qian, H., Inouye, M., Ikura, M.

(1999) Nat Struct Biol 6: 729-734

Released	2000-01-12
Method	SOLUTION NMR
Organisms	Escherichia coli
Macromolecule	PROTEIN (ENVZ_ECOLI) (protein)

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1MUJ \| pdb_00001muj	Download File View File

Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide

Zhu, Y., Wilson, I.A.

(2003) J Mol Biology 326: 1157-1174

Released	2003-02-18
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	CLIP peptide (protein) H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN (protein) H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN (protein)
Unique Ligands	NAG

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1PQ0 \| pdb_00001pq0	Download File View File

Crystal structure of mouse Bcl-xl

Liu, X., Dai, S., Zhu, Y., Marrack, P., Kappler, J.W.

(2003) Immunity 19: 341-352

Released	2003-09-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Mus musculus
Macromolecule	Apoptosis regulator Bcl-X (protein)

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1PQ1 \| pdb_00001pq1	Download File View File

Crystal structure of Bcl-xl/Bim

Liu, X., Dai, S., Zhu, Y., Marrack, P., Kappler, J.W.

(2003) Immunity 19: 341-352

Released	2003-09-23
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Mus musculus
Macromolecule	Apoptosis regulator Bcl-X (protein) BCL2-like protein 11 (protein)

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1SBW \| pdb_00001sbw	Download File View File

CRYSTAL STRUCTURE OF MUNG BEAN INHIBITOR LYSINE ACTIVE FRAGMENT COMPLEX WITH BOVINE BETA-TRYPSIN AT 1.8A RESOLUTION

Huang, Q., Zhu, Y., Chi, C., Tang, Y.

(1999) J Biomol Struct Dyn 16: 1219-1224

Released	1999-05-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus Vigna radiata
Macromolecule	PROTEIN (BETA-TRYPSIN) (protein) PROTEIN (MUNG BEAN INHIBITOR LYSIN ACTIVE FRAGMENT) (protein)
Unique Ligands	CA, SO4

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1XDO \| pdb_00001xdo	Download File View File

Crystal Structure of Escherichia coli Polyphosphate Kinase

Zhu, Y., Huang, W., Lee, S.S., Xu, W.

(2005) EMBO Rep 6: 681-687

Released	2005-06-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	Polyphosphate kinase (protein)

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1XDP \| pdb_00001xdp	Download File View File

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

Zhu, Y., Huang, W., Lee, S.S., Xu, W.

(2005) EMBO Rep 6: 681-687

Released	2005-06-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	Polyphosphate kinase (protein)
Unique Ligands	ATP, MG

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1ZUC \| pdb_00001zuc	Download File View File

Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist tanaproget

Zhang, Z., Olland, A.M., Zhu, Y., Cohen, J., Berrodin, T., Chippari, S., Appavu, C., Li, S., Wilhem, J., Chopra, R., Fensome, A., Zhang, P., Wrobel, J., Unwalla, R.J., Lyttle, C.R., Winneker, R.C.

(2005) J Biological Chem 280: 28468-28475

Released	2005-07-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Progesterone receptor (protein)
Unique Ligands	SO4, T98

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2N9X \| pdb_00002n9x	Download File View File

LC3 FUNDC1 complex structure

Xia, B., Kuang, Y.

(2016) Autophagy 12: 2363-2373

Released	2016-12-14
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	FUN14 domain-containing protein 1 (protein) Microtubule-associated proteins 1A/1B light chain 3B (protein)

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2NNQ \| pdb_00002nnq	Download File View File

Crystal structure of human adipocyte fatty acid binding protein in complex with ((2'-(5-ethyl-3,4-diphenyl-1H-pyrazol-1-yl)-3-biphenylyl)oxy)acetic acid

Jacobson, B.L.

(2007) Bioorg Med Chem Lett 17: 3511-3515

Released	2007-06-12
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Fatty acid-binding protein, adipocyte (protein)
Unique Ligands	SO4, T4B

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2P1W \| pdb_00002p1w	Download File View File

structure of the phosphothreonine lyase SpvC, the effector protein from Salmonella

Zhu, Y., Wang, D.C., Shao, F.

(2007) Mol Cell 28: 899-913

Released	2007-12-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Salmonella enterica subsp. enterica serovar Enteritidis
Macromolecule	27.5 kDa virulence protein (protein)

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2P8V \| pdb_00002p8v	Download File View File

Crystal structure of human Homer3 EVH1 domain

Bouyain, S., Tu, J., Huang, G.N., Worley, P.F., Leahy, D.

(2008) Science 319: 476-481

Released	2007-11-20
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Homo sapiens
Macromolecule	Homer protein homolog 3 (protein)
Unique Ligands	SO4

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2PJT \| pdb_00002pjt	Download File View File

Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344

Xu, Z., Huang, A., Lovering, F., Levin, J.I., Mosyak, L.

(2007) Bioorg Med Chem 15: 6170-6181

Released	2008-04-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Collagenase 3 (protein)
Unique Ligands	347, CA, ZN

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2Q8Y \| pdb_00002q8y	Download File View File

Structural insight into the enzymatic mechanism of the phophothreonine lyase

Zhu, Y.-Q., Wang, D.-C., Shao, F.

(2007) Mol Cell 28: 899-913

Released	2007-12-11
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens Salmonella enterica subsp. enterica serovar Enteritidis
Macromolecule	27.5 kDa virulence protein (protein) Mitogen-activated protein kinase 7 (protein)

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2QW1 \| pdb_00002qw1	Download File View File

Glucose/galactose binding protein bound to 3-O-methyl D-glucose

Borrok, M.J., Kiessling, L.L., Forest, K.T.

(2009) ACS Chem Biol 4: 447-456

Released	2008-08-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	D-galactose-binding periplasmic protein (protein)
Unique Ligands	3MG, CA, NA

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2V0H \| pdb_00002v0h	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	CO, PEG, SO4

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2V0I \| pdb_00002v0i	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	PEG, PG4, SO4, UD1

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2V0J \| pdb_00002v0j	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	H2U, MG, PG4, PGE, SO4

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2V0K \| pdb_00002v0k	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	PG4, PGE, SO4, UDP

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2V0L \| pdb_00002v0l	Download File View File

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Mochalkin, I., Lightle, S., Ohren, J.F., Chirgadze, N.Y.

(2007) Protein Sci 16: 2657

Released	2008-01-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Haemophilus influenzae
Macromolecule	BIFUNCTIONAL PROTEIN GLMU (protein)
Unique Ligands	PG4, PGE, SO4, URI

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2WVX \| pdb_00002wvx	Download File View File

Structure of the Family GH92 Inverting Mannosidase BT3990 from Bacteroides thetaiotaomicron VPI-5482

Suits, M.D.L., Zhu, Y., Thompson, A., Gilbert, H.J., Davies, G.J.

(2010) Nat Chem Biol 6: 125

Released	2009-11-03
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	PUTATIVE ALPHA-1,2-MANNOSIDASE (protein)
Unique Ligands	CA, GOL