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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Nikolov, D.B."

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Search Summary

This query matches 46 Structures.

Refinements

Structure Determination Methodology

experimental (46)

Scientific Name of Source Organism

	Homo sapiens (20)
	Mus musculus (9)
	Salmonella enterica (5)
	Arabidopsis thaliana (3)
	Bos taurus (3)
	Cedar virus (3)
	Gallus gallus (3)
	Henipavirus nipahense (3)
	Henipavirus hendraense (2)
	Chlorella virus (1)

More...

Taxonomy

	Eukaryota (34)
	Riboviria (8)
	Bacteria (7)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (45)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (46)
	DNA (3)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (16)
	2.5 - 3.0 (13)
	3.0 - 3.5 (9)
	3.5 - 4.0 (3)
	> 4.5 (1)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (10)
	2005 - 2009 (11)
	2010 - 2014 (11)
	2015 - 2019 (7)
	2020 - 2024 (3)

Enzyme Classification Name

	Transferases (18)
	Hydrolases (6)
	Ligases (1)
	Oxidoreductases (1)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (36)
	Cyclic (12)
	Dihedral (4)

SCOP Classification

	All beta proteins (12)
	Alpha and beta proteins (a+b) (11)
	Artifacts (5)
	Alpha and beta proteins (a/b) (7)
	All alpha proteins (1)

AllSelected

1 to 25 of 46 Structures

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1CDW \| pdb_00001cdw	Download File View File

HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA

Nikolov, D.B., Chen, H., Halay, E.D., Hoffmann, A., Roeder, R.G., Burley, S.K.

(1996) Proc Natl Acad Sci U S A 93: 4862-4867

Released	1996-12-23
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	PROTEIN (TATA BINDING PROTEIN (TBP)) (protein) DNA (5'-D(CPAPGPCPCPTPTPTPTPAPTPAPGPCPAPG)-3') (nucleic acid) DNA (5'-D(CPTPGPCPTPAPTPAPAPAPAPGPGPCPTPG)-3') (nucleic acid)

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1FVI \| pdb_00001fvi	Download File View File

CRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE

Odell, M., Sriskanda, V., Shuman, S., Nikolov, D.B.

(2000) Mol Cell 6: 1183-1193

Released	2000-11-22
Method	X-RAY DIFFRACTION 2 Å
Organisms	Chlorella virus
Macromolecule	CHLORELLA VIRUS DNA LIGASE-ADENYLATE (protein)
Unique Ligands	AMP, SO4

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1IIM \| pdb_00001iim	Download File View File

thymidylyltransferase complexed with TTP

Barton, W.A., Lesniak, J., Biggins, J.B., Jeffrey, P.D., Jiang, J., Rajashankar, K.R., Thorson, J.S., Nikolov, D.B.

(2001) Nat Struct Biol 8: 545-551

Released	2001-05-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica
Macromolecule	glucose-1-phosphate thymidylyltransferase (protein)
Unique Ligands	TTP

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1IIN \| pdb_00001iin	Download File View File

thymidylyltransferase complexed with UDP-glucose

Barton, W.A., Lesniak, J., Biggins, J.B., Jeffrey, P.D., Jiang, J., Rajashankar, K.R., Thorson, J.S., Nikolov, D.B.

(2001) Nat Struct Biol 8: 545-551

Released	2001-05-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Salmonella enterica
Macromolecule	glucose-1-phosphate thymidylyltransferase (protein)
Unique Ligands	UPG

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1KGY \| pdb_00001kgy	Download File View File

Crystal Structure of the EphB2-ephrinB2 complex

Himanen, J.P., Rajashankar, K.R., Lackmann, M., Cowan, C.A., Henkemeyer, M., Nikolov, D.B.

(2001) Nature 414: 933-938

Released	2002-05-28
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Mus musculus
Macromolecule	EPHRIN TYPE-B RECEPTOR 2 (protein) EPHRIN-B2 (protein)

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1MP3 \| pdb_00001mp3	Download File View File

L89T VARIANT OF S. ENTERICA RmlA

Barton, W.A., Biggins, J.B., Jiang, J., Thorson, J.T., Nikolov, D.B.

(2002) Proc Natl Acad Sci U S A 99: 13397-13402

Released	2002-10-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Salmonella enterica
Macromolecule	GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (protein)
Unique Ligands	TTP

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1MP4 \| pdb_00001mp4	Download File View File

W224H VARIANT OF S. ENTERICA RmlA

Barton, W.A., Biggins, J.B., Jiang, J., Thorson, J.S., Nikolov, D.B.

(2002) Proc Natl Acad Sci U S A 99: 13397-13402

Released	2002-10-09
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Salmonella enterica
Macromolecule	W224H Variant of S. Enterica RmlA Bound to UDP-Glucose (protein)
Unique Ligands	UPG

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1MP5 \| pdb_00001mp5	Download File View File

Y177F VARIANT OF S. ENTERICA RmlA

Barton, W.A., Biggins, J.B., Jiang, J., Thorson, J.S., Nikolov, D.B.

(2002) Proc Natl Acad Sci U S A 99: 13397-13402

Released	2002-10-09
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Salmonella enterica
Macromolecule	Y177F VARIANT OF S. ENTERICA RmlA BOUND TO UDP-GLUCOSE (protein)
Unique Ligands	UPG

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1N2F \| pdb_00001n2f	Download File View File

CRYSTAL STRUCTURE OF P. AERUGINOSA OHR

Lesniak, J., Barton, W.A., Nikolov, D.B.

(2002) EMBO J 21: 6649-6659

Released	2002-12-25
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Organic Hydroperoxide Resistance Protein (protein)
Unique Ligands	DTT

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1NUK \| pdb_00001nuk	Download File View File

CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEPTOR TYROSINE KINASE

Himanen, J.-P., Henkemeyer, M., Nikolov, D.B.

(1998) Nature 396: 486-491

Released	1999-10-13
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Mus musculus
Macromolecule	PROTEIN (TYROSINE-PROTEIN KINASE RECEPTOR EPH) (protein)

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1P8T \| pdb_00001p8t	Download File View File

Crystal structure of Nogo-66 Receptor

Barton, W.A., Liu, B.P., Tzvetkova, D., Jeffrey, P.D., Fournier, A.E., Sah, D., Cate, R., Strittmatter, S.M., Nikolov, D.B.

(2003) EMBO J 22: 3291-3302

Released	2003-05-20
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Reticulon 4 receptor (protein)
Unique Ligands	NAG, NDG

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1QWI \| pdb_00001qwi	Download File View File

Crystal Structure of E. coli OsmC

Lesniak, J., Barton, W.A., Nikolov, D.B.

(2003) Protein Sci 12: 2838-2843

Released	2003-12-16
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Escherichia coli
Macromolecule	osmotically inducible protein (protein)

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1SHX \| pdb_00001shx	Download File View File

Ephrin A5 ligand structure

Himanen, J.P., Barton, W.A., Nikolov, D.B., Jeffrey, P.D.

(2005) J Biological Chem 280: 26526-26532

Released	2005-04-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Ephrin-A5 (protein)
Unique branched monosaccharides	NAG

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1VOK \| pdb_00001vok	Download File View File

ARABIDOPSIS THALIANA TBP (DIMER)

Nikolov, D.B., Burley, S.K.

(1994) Nat Struct Biol 1: 621-637

Released	1996-11-08
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Arabidopsis thaliana
Macromolecule	TATA-BOX-BINDING PROTEIN (protein)
Unique Ligands	SO4

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1VOL \| pdb_00001vol	Download File View File

TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX

Nikolov, D.B., Chen, H., Halay, E.D., Usheva, A.U., Hisatake, K., Lee, D.K., Roeder, R.G., Burley, S.K.

(1995) Nature 377: 119-128

Released	1996-11-08
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Arabidopsis thaliana Homo sapiens
Macromolecule	PROTEIN (TATA BINDING PROTEIN (TBP)) (protein) PROTEIN (TRANSCRIPTION FACTOR IIB (TFIIB)) (protein) DNA (5'-D(CPAPGPCPCPCPTPTPTPTPAPTPAPGPCPC)-3') (nucleic acid) DNA (5'-D(GPGPCPTPAPTPAPAPAPAPGPGPGPCPTPG)-3') (nucleic acid)

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1VTL \| pdb_00001vtl	Download File View File

CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TATA ELEMENT

Kim, J.L., Nikolov, D.B., Burley, S.K.

(1993) Nature 365: 520-527

Released	2011-07-13
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Arabidopsis thaliana
Macromolecule	TATA BINDING PROTEIN (TBP) (protein) DNA (5'-D(GPCPTPAPTPAPAPAPAPGPGPGPCPA)-3') (nucleic acid) DNA (5'-D(TPGPCPCPCPTPTPTPTPAPTPAPGPC)-3') (nucleic acid)

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1Z3S \| pdb_00001z3s	Download File View File

Angiopoietin-2 Receptor Binding Domain

Barton, W.A., Tzvetkova, D., Nikolov, D.B.

(2005) Structure 13: 825-832

Released	2005-07-12
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Homo sapiens
Macromolecule	Angiopoietin-2 (protein)
Unique Ligands	CA

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1Z3U \| pdb_00001z3u	Download File View File

Structure of the Angiopoietin-2 Recptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition

Barton, W.A., Tzvetkova, D., Nikolov, D.B.

(2005) Structure 13: 825-832

Released	2005-07-12
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	Angiopoietin-2 (protein)
Unique Ligands	CA

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2AO7 \| pdb_00002ao7	Download File View File

Adam10 Disintegrin and cysteine- rich domain

Janes, P.W., Saha, N., Barton, W.A., Kolev, M.V., Wimmer-Kleikamp, S.H., Nievergall, E., Blobel, C.P., Himanen, J.-P., Lackmann, M., Nikolov, D.B.

(2005) Cell 123: 291-304

Released	2006-08-08
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Bos taurus
Macromolecule	ADAM 10 (protein)
Unique Ligands	SO4

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2GY5 \| pdb_00002gy5	Download File View File

Tie2 Ligand-Binding Domain Crystal Structure

Barton, W.A., Nikolov, D.B.

(2006) Nat Struct Mol Biol 13: 524-532

Released	2006-06-06
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	Angiopoietin-1 receptor (protein)
Unique Ligands	NAG, NDG, SO4

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2GY7 \| pdb_00002gy7	Download File View File

Angiopoietin-2/Tie2 Complex Crystal Structure

Barton, W.A., Nikolov, D.B.

(2006) Nat Struct Mol Biol 13: 524-532

Released	2006-06-06
Method	X-RAY DIFFRACTION 3.7 Å
Organisms	Homo sapiens
Macromolecule	Angiopoietin-1 receptor (protein) Angiopoietin-2 (protein)
Unique Ligands	CA, NAG, SO4
Unique branched monosaccharides	NAG, NDG

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3D11 \| pdb_00003d11	Download File View File

Crystal Structures of the Nipah G Attachment Glycoprotein

Xu, K., Rajashankar, K.R., Chan, Y.P., Himanen, P., Broder, C.C., Nikolov, D.B.

(2008) Proc Natl Acad Sci U S A 105: 9953-9958

Released	2008-08-19
Method	X-RAY DIFFRACTION 2.306 Å
Organisms	Henipavirus nipahense
Macromolecule	Hemagglutinin-neuraminidase (protein)
Unique Ligands	IOD, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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3D12 \| pdb_00003d12	Download File View File

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

Xu, K., Rajashankar, K.R., Chan, Y.P., Himanen, P., Broder, C.C., Nikolov, D.B.

(2008) Proc Natl Acad Sci U S A 105: 9953-9958

Released	2008-08-19
Method	X-RAY DIFFRACTION 3.005 Å
Organisms	Henipavirus nipahense Mus musculus
Macromolecule	Ephrin-B3 (protein) Hemagglutinin-neuraminidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	BGC, BMA, GL0, GLC, GXL, LXB, LXZ, MAN, NAG, NGA, NGZ