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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Sivaraman, J."

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Search Summary

This query matches 181 Structures.

Refinements

Structure Determination Methodology

experimental (181)

Scientific Name of Source Organism

	Homo sapiens (60)
	Escherichia coli (26)
	Mus musculus (9)
	Streptomyces coelicolor (8)
	Streptococcus pyogenes (5)
	Nanoarchaeum equitans Kin4-M (4)
	Paslahepevirus balayani (4)
	Shrimp white spot syndrome virus (4)
	Thermotoga maritima (4)
	Aedes aegypti (3)

More...

Taxonomy

	Eukaryota (93)
	Bacteria (77)
	Riboviria (6)
	Archaea (5)
	Viruses incertae sedis (4)
	Eukaryota (eukaryotes) (2)
	Varidnaviria (1)
	other sequences (1)

Experimental Method

	X-RAY DIFFRACTION (165)
	ELECTRON MICROSCOPY (11)
	SOLUTION NMR (5)

Polymer Entity Type

	Protein (181)
	RNA (2)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (34)
	2.0 - 2.5 (65)
	2.5 - 3.0 (54)
	3.0 - 3.5 (12)
	3.5 - 4.0 (4)
	4.0 - 4.5 (2)
	> 4.5 (2)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (31)
	2005 - 2009 (44)
	2010 - 2014 (48)
	2015 - 2019 (30)
	2020 - 2024 (24)

Enzyme Classification Name

	Transferases (41)
	Hydrolases (45)
	Oxidoreductases (17)
	Isomerases (14)
	Ligases (12)
	Lyases (8)
	Translocases (3)

Membrane Protein Annotation

OPM (3)

Symmetry Type

	Asymmetric (97)
	Cyclic (63)
	Dihedral (17)
	Octahedral (9)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (28)
	Alpha and beta proteins (a+b) (35)
	All beta proteins (16)
	All alpha proteins (11)
	Artifacts (14)
	Multi-domain proteins (alpha and beta) (11)
	Small proteins (6)

AllSelected

1 to 25 of 181 Structures

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1CJL \| pdb_00001cjl	Download File View File

CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM

Coulombe, R., Grochulski, P., Sivaraman, J., Cygler, M.

(1996) EMBO J 15: 5492-5503

Released	1997-08-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	PROCATHEPSIN L (protein)

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1CS8 \| pdb_00001cs8	Download File View File

CRYSTAL STRUCTURE OF PROCATHEPSIN L

Cygler, M., Coulombe, R.

(1996) EMBO J 15: 5492-5503

Released	1999-08-23
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	HUMAN PROCATHEPSIN L (protein)

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1DEU \| pdb_00001deu	Download File View File

CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE

Sivaraman, J., Nagler, D.K., Zhang, R., Menard, R., Cygler, M.

(2000) J Mol Biology 295: 939-951

Released	2000-02-18
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	PROCATHEPSIN X (protein)

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1EOJ \| pdb_00001eoj	Download File View File

Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures

Slon-Usakiewicz, J.J., Sivaraman, J., Li, Y., Cygler, M., Konishi, Y.

(2000) Biochemistry 39: 2384-2391

Released	2000-05-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ALPHA THROMBIN (protein) THROMBIN INHIBITOR P798 (protein)

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1EOL \| pdb_00001eol	Download File View File

Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures

Slon-Usakiewicz, J.J., Sivaraman, J., Li, Y., Cygler, M., Konishi, Y.

(2000) Biochemistry 39: 2384-2391

Released	2000-05-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	ALPHA THROMBIN (protein) THROMBIN INHIBITOR P628 (protein)

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1FC4 \| pdb_00001fc4	Download File View File

2-AMINO-3-KETOBUTYRATE COA LIGASE

Schmidt, A., Matte, A., Li, Y., Sivaraman, J., Larocque, R., Schrag, J.D., Smith, C., Sauve, V., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2001) Biochemistry 40: 5151-5160

Released	2001-05-02
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	2-AMINO-3-KETOBUTYRATE CONENZYME A LIGASE (protein)
Unique Ligands	AKB, PLP

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1FC5 \| pdb_00001fc5	Download File View File

CRYSTAL STRUCTURE OF MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN

Huang, W., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2001) J Mol Biology 310: 419-431

Released	2001-07-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN (protein)
Unique Ligands	MG

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1FG3 \| pdb_00001fg3	Download File View File

CRYSTAL STRUCTURE OF L-HISTIDINOL PHOSPHATE AMINOTRANSFERASE COMPLEXED WITH L-HISTIDINOL

Sivaraman, J., Cygler, M.

(2001) J Mol Biology 311: 761-776

Released	2001-08-22
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	HISTIDINOL PHOSPHATE AMINOTRANSFERASE (protein)
Unique Ligands	HSA, PLP

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1FG7 \| pdb_00001fg7	Download File View File

CRYSTAL STRUCTURE OF L-HISTIDINOL PHOSPHATE AMINOTRANSFERASE WITH PYRIDOXAL-5'-PHOSPHATE

Sivaraman, J., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2001) J Mol Biology 311: 761-776

Released	2001-08-22
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Escherichia coli
Macromolecule	HISTIDINOL PHOSPHATE AMINOTRANSFERASE (protein)
Unique Ligands	PMP

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1H1C \| pdb_00001h1c	Download File View File

Histidinol-phosphate aminotransferase (HisC) from Thermotoga maritima

Vega, M.C., Fernandez, F.J., Wilmanns, M.

(2004) J Biological Chem 279: 21478

Released	2004-03-19
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Thermotoga maritima
Macromolecule	HISTIDINOL-PHOSPHATE AMINOTRANSFERASE (protein)
Unique Ligands	PLP

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1IJI \| pdb_00001iji	Download File View File

Crystal Structure of L-Histidinol Phosphate Aminotransferase with PLP

Sivaraman, J., Li, Y., Larocque, R., Schrag, J.D., Cygler, M., Matte, A.

(2001) J Mol Biology 311: 761-776

Released	2001-08-29
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	Histidinol Phosphate Aminotransferase (protein)
Unique Ligands	PLP

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1K75 \| pdb_00001k75	Download File View File

The L-histidinol dehydrogenase (hisD) structure implicates domain swapping and gene duplication.

Barbosa, J.A.R.G., Sivaraman, J., Li, Y., Larocque, R., Matte, A., Schrag, J., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2002) Proc Natl Acad Sci U S A 99: 1859-1864

Released	2002-02-27
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Escherichia coli
Macromolecule	L-histidinol dehydrogenase (protein)
Unique Ligands	GOL, SO4

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1KAE \| pdb_00001kae	Download File View File

L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINOL (SUBSTRATE), ZINC AND NAD (COFACTOR)

Barbosa, J.A.R.G., Sivaraman, J., Li, Y., Larocque, R., Matte, A., Schrag, J.D., Cygler, M.

(2002) Proc Natl Acad Sci U S A 99: 1859-1864

Released	2002-06-12
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	Histidinol dehydrogenase (protein)
Unique Ligands	DTT, GOL, HSO, IMD, NAD, SO4, ZN

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1KAH \| pdb_00001kah	Download File View File

L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINE (PRODUCT), ZN AND NAD (COFACTOR)

Barbosa, J.A.R.G., Sivaraman, J., Li, Y., Larocque, R., Matte, A., Schrag, J.D., Cygler, M.

(2002) Proc Natl Acad Sci U S A 99: 1859-1864

Released	2002-06-12
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	Histidinol dehydrogenase (protein)
Unique Ligands	HIS, ZN

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1KAR \| pdb_00001kar	Download File View File

L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH HISTAMINE (INHIBITOR), ZINC AND NAD (COFACTOR)

Barbosa, J.A.R.G., Sivaraman, J., Li, Y., Larocque, R., Matte, A., Schrag, J.D., Cygler, M.

(2002) Proc Natl Acad Sci U S A 99: 1859-1864

Released	2002-06-12
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	Histidinol dehydrogenase (protein)
Unique Ligands	HSM, ZN

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1KSK \| pdb_00001ksk	Download File View File

STRUCTURE OF RSUA

Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M., Matte, A.

(2002) Nat Struct Biol 9: 353-358

Released	2002-04-24
Method	X-RAY DIFFRACTION 2 Å
Organisms	Escherichia coli
Macromolecule	RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A (protein)
Unique Ligands	URA

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1KSL \| pdb_00001ksl	Download File View File

STRUCTURE OF RSUA

Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M., Matte, A., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2002) Nat Struct Biol 9: 353-358

Released	2002-04-24
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Escherichia coli
Macromolecule	RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A (protein)
Unique Ligands	URA

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1KSV \| pdb_00001ksv	Download File View File

STRUCTURE OF RSUA

Sivaraman, J., Sauve, V., Larocque, R., Stura, E.A., Schrag, J.D., Cygler, M., Matte, A.

(2002) Nat Struct Biol 9: 353-358

Released	2002-04-24
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Escherichia coli
Macromolecule	RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A (protein)
Unique Ligands	U5P

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1LKZ \| pdb_00001lkz	Download File View File

Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli.

Rangarajan, E.S., Sivaraman, J., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2002) Proteins 48: 737-740

Released	2002-05-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	Ribose 5-phosphate isomerase A (protein)

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1MC3 \| pdb_00001mc3	Download File View File

CRYSTAL STRUCTURE OF RFFH

Sivaraman, J., Sauve, V., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

(2002) J Biological Chem 277: 44214-44219

Released	2002-11-20
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli
Macromolecule	GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (protein)
Unique Ligands	MG, TTP

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1MHW \| pdb_00001mhw	Download File View File

Design of non-covalent inhibitors of human cathepsin L. From the 96-residue proregion to optimized tripeptides

Chowdhury, S., Sivaraman, J., Wang, J., Devanathan, G., Lachance, P., Qi, H., Menard, R., Lefebvre, J., Konishi, Y., Cygler, M., Sulea, T., Purisima, E.O.

(2002) J Med Chem 45: 5321-5329

Released	2002-12-11
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	4-biphenylacetyl-Cys-(D)Arg-Tyr-N-(2-phenylethyl) amide (protein) Cathepsin L (protein)