RCSB PDB: Search

Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.

Help

Help

RCSB PDB

Deposit
- PDBx/mmCIF file
- pdb_extract
- SF-Tool
- Ligand Expo
- MAXIT
- Validation Server
- Validation API
- Information for Journals
- Validation Task Forces
- wwPDB OneDep System
- PDB-IHM
Search
Visualize
Analyze
Download
Learn
- Training Courses
- Guide to PDB Data
- Molecule of the Month
- Educational Resources
- Curricula
- Browse
- News
- SciArt Galleries
- Irving Geis
- David Goodsell
About
Careers
COVID-19

233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

	Include CSM
Advanced Search \| Browse Annotations		Help

Search
Query History
Browse Annotations
MyPDB

QUERY: Structure Author = "Nyborg, J."

MyPDB Login

Search API

Advanced Search Query Builder

Help

Full Text

Structure Attributes

Help

NOT

Count

Add Subquery

Chemical Attributes

Sequence Similarity

Sequence Motif

Structure Similarity

Structure Motif

Chemical Similarity

Return

grouped by

Include Computed Structure Models (CSM)

Count

Clear

Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Saccharomyces cerevisiae (7)
	Thermus aquaticus (5)
	Bos taurus (4)
	Homo sapiens (3)
	Thermus thermophilus HB8 (3)
	Escherichia coli BL21 (2)
	Escherichia coli (1)
	Escherichia coli K-12 (1)
	Planobispora rosea (1)
	Streptomyces murinus (1)

Taxonomy

	Eukaryota (14)
	Bacteria (12)

Experimental Method

	X-RAY DIFFRACTION (23)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (24)
	RNA (4)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (5)
	2.0 - 2.5 (5)
	2.5 - 3.0 (7)
	3.0 - 3.5 (4)
	> 4.5 (1)

Release Date

	1985 - 1989 (1)
	1990 - 1994 (2)
	1995 - 1999 (8)
	2000 - 2004 (7)
	2005 - 2009 (6)

Enzyme Classification Name

	Hydrolases (5)
	Isomerases (1)
	Ligases (1)

Symmetry Type

	Asymmetric (18)
	Cyclic (5)
	Dihedral (1)

SCOP Classification

	All beta proteins (16)
	Alpha and beta proteins (a/b) (18)
	All alpha proteins (5)
	Alpha and beta proteins (a+b) (5)

AllSelected

1 to 24 of 24 Structures

Page 1 of 1

Sort by

Explore in 3D

1AYO \| pdb_00001ayo	Download File View File

RECEPTOR BINDING DOMAIN OF BOVINE ALPHA-2-MACROGLOBULIN

Jenner, L.B., Husted, L., Thirup, S., Sottrup-Jensen, L., Nyborg, J.

(1998) Structure 6: 595-604

Released	1998-11-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	ALPHA-2-MACROGLOBULIN (protein)
Unique Ligands	CA
Unique branched monosaccharides	NAG

Explore in 3D

1B23 \| pdb_00001b23	Download File View File

E. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:GTP ternary complex

Nissen, P., Kjeldgaard, M., Thirup, S., Nyborg, J.

(1999) Structure 7: 143-156

Released	1998-12-07
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Escherichia coli Thermus aquaticus
Macromolecule	ELONGATION FACTOR TU (protein) CYSTEINYL TRNA (nucleic acid)
Unique Ligands	CYS, GNP, MG, SO4

Explore in 3D

1D2E \| pdb_00001d2e	Download File View File

CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP

Andersen, G.R., Thirup, S., Spremulli, L.L., Nyborg, J.

(2000) J Mol Biology 297: 421-436

Released	1999-09-28
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Bos taurus
Macromolecule	ELONGATION FACTOR TU (EF-TU) (protein)
Unique Ligands	GDP, MG

Explore in 3D

1DXI \| pdb_00001dxi	Download File View File

STRUCTURE DETERMINATION OF GLUCOSE ISOMERASE FROM STREPTOMYCES MURINUS AT 2.6 ANGSTROMS RESOLUTION

Rasmussen, H., La Cour, T., Nyborg, J., Schulein, M.

(1994) Acta Crystallogr D Biol Crystallogr 50: 124-131

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Streptomyces murinus
Macromolecule	D-XYLOSE ISOMERASE (protein)
Unique Ligands	MG

Explore in 3D

1EFT \| pdb_00001eft	Download File View File

THE CRYSTAL STRUCTURE OF ELONGATION FACTOR EF-TU FROM THERMUS AQUATICUS IN THE GTP CONFORMATION

Kjeldgaard, M., Nissen, P., Thirup, S., Nyborg, J.

(1993) Structure 1: 35-50

Released	1994-08-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus aquaticus
Macromolecule	ELONGATION FACTOR TU (protein)
Unique Ligands	GNP, MG

Explore in 3D

1ETU \| pdb_00001etu	Download File View File

STRUCTURAL DETAILS OF THE BINDING OF GUANOSINE DIPHOSPHATE TO ELONGATION FACTOR TU FROM E. COLI AS STUDIED BY X-RAY CRYSTALLOGRAPHY

Clark, B.F.C., Lacour, T.F.M., Kjeldgaard, M., Morikawa, K., Nyborg, J., Rubin, R., Thirup, S.

(1985) EMBO J 4: 2385-2388

Released	1988-07-16
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Escherichia coli K-12
Macromolecule	ELONGATION FACTOR TU (protein)
Unique Ligands	GDP, MG

Explore in 3D

1F60 \| pdb_00001f60	Download File View File

CRYSTAL STRUCTURE OF THE YEAST ELONGATION FACTOR COMPLEX EEF1A:EEF1BA

Andersen, G.R., Pedersen, L., Valente, L., Kinzy, T.G., Nyborg, J.

(2000) Mol Cell 6: 1261-1266

Released	2000-07-04
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ELONGATION FACTOR EEF1A (protein) ELONGATION FACTOR EEF1BA (protein)

Explore in 3D

1G7C \| pdb_00001g7c	Download File View File

YEAST EEF1A:EEF1BA IN COMPLEX WITH GDPNP

Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G., Nyborg, J.

(2001) Nat Struct Biol 8: 531-534

Released	2000-12-06
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	ELONGATION FACTOR 1-ALPHA (protein) ELONGATION FACTOR 1-BETA (protein)
Unique Ligands	5GP

Explore in 3D

1IJE \| pdb_00001ije	Download File View File

Nucleotide Exchange Intermediates in the eEF1A-eEF1Ba Complex

Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G., Nyborg, J.

(2001) Nat Struct Biol 8: 531-534

Released	2001-05-09
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	elongation factor 1-alpha (protein) elongation factor 1-beta (protein)
Unique Ligands	GDP

Explore in 3D

1IJF \| pdb_00001ijf	Download File View File

Nucleotide exchange mechanisms in the eEF1A-eEF1Ba complex

Andersen, G.R., Valente, L., Pedersen, L., Kinzy, T.G., Nyborg, J.

(2001) Nat Struct Biol 8: 531-534

Released	2001-05-09
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	elongation factor 1-alpha (protein) elongation factor 1-beta (protein)
Unique Ligands	GDP, MG

Explore in 3D

1NHY \| pdb_00001nhy	Download File View File

Crystal Structure of the GST-like Domain of Elongation Factor 1-gamma from Saccharomyces cerevisiae.

Jeppesen, M.G., Ortiz, P., Kinzy, T.G., Andersen, G.R., Nyborg, J.

(2003) J Biological Chem 278: 47190-47198

Released	2003-01-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Elongation factor 1-gamma 1 (protein)
Unique Ligands	SO4

Explore in 3D

1OB2 \| pdb_00001ob2	Download File View File

E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA

Kristensen, O., Nissen, P., Nyborg, J.

To be published

Released	2004-05-27
Method	X-RAY DIFFRACTION 3.35 Å
Organisms	Escherichia coli BL21 Saccharomyces cerevisiae
Macromolecule	ELONGATION FACTOR TU (protein) TRANSFER-RNA, PHE (nucleic acid)
Unique Ligands	GNP, KIR, MG
Unique branched monosaccharides	FRU, GLC

Explore in 3D

1OB5 \| pdb_00001ob5	Download File View File

T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA

Dahlberg, C., Nielsen, R.C., Parmeggiani, A., Nyborg, J., Nissen, P.

(2006) J Biological Chem 281: 2893

Released	2005-10-13
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Saccharomyces cerevisiae Thermus aquaticus
Macromolecule	ELONGATION FACTOR TU (protein) TRANSFER-RNA, PHE (nucleic acid)
Unique Ligands	ENX, GNP, MG

Explore in 3D

1PSR \| pdb_00001psr	Download File View File

HUMAN PSORIASIN (S100A7)

Brodersen, D.E., Etzerodt, M., Madsen, P., Celis, J., Thoegersen, H.C., Nyborg, J., Kjeldgaard, M.

(1998) Structure 6: 477-489

Released	1999-01-13
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Homo sapiens
Macromolecule	PSORIASIN (protein)
Unique Ligands	HO

Explore in 3D

1TTT \| pdb_00001ttt	Download File View File

Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex

Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F.C., Nyborg, J.

(1995) Science 270: 1464-1472

Released	1996-12-23
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus aquaticus
Macromolecule	OF ELONGATION FACTOR TU (EF-TU) (protein) TRANSFER RIBONUCLEIC ACID (YEAST, PHE) (nucleic acid)
Unique Ligands	GNP, MG, PHE

Explore in 3D

1TUI \| pdb_00001tui	Download File View File

INTACT ELONGATION FACTOR TU IN COMPLEX WITH GDP

Polekhina, G., Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C., Nyborg, J.

(1996) Structure 4: 1141-1151

Released	1997-06-05
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Thermus aquaticus
Macromolecule	ELONGATION FACTOR TU (protein)
Unique Ligands	GDP, MG

Explore in 3D

1WLE \| pdb_00001wle	Download File View File

Crystal Structure of mammalian mitochondrial seryl-tRNA synthetase complexed with seryl-adenylate

Chimnaronk, S., Jeppesen, M.G., Suzuki, T., Nyborg, J., Watanabe, K.

(2005) EMBO J 24: 3369-3379

Released	2005-09-06
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Bos taurus
Macromolecule	Seryl-tRNA synthetase (protein)
Unique Ligands	SRP

Explore in 3D

1XB2 \| pdb_00001xb2	Download File View File

Crystal Structure of Bos taurus mitochondrial Elongation Factor Tu/Ts Complex

Jeppesen, M.G., Navratil, T., Spremulli, L.L., Nyborg, J.

(2005) J Biological Chem 280: 5071-5081

Released	2004-11-23
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Bos taurus
Macromolecule	Elongation factor Ts, mitochondrial (protein) Elongation factor Tu, mitochondrial (protein)

Explore in 3D

2BVN \| pdb_00002bvn	Download File View File

E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa

Parmeggiani, A., Krab, I.M., Watanabe, T., Nielsen, R.C., Dahlberg, C., Nyborg, J., Nissen, P.

(2006) J Biological Chem 281: 2893

Released	2005-09-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli BL21
Macromolecule	ELONGATION FACTOR TU (protein)
Unique Ligands	ENX, GNP, MG

Explore in 3D

2C77 \| pdb_00002c77	Download File View File

EF-Tu complexed with a GTP analog and the antibiotic GE2270 A

Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R.C., Nyborg, J., Nissen, P.

(2006) Biochemistry 45: 6846-6857

Released	2006-03-16
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Planobispora rosea Thermus thermophilus HB8
Macromolecule	ELONGATION FACTOR TU-B (protein) THIOCILLIN GE2270 (protein)
Unique Ligands	GNP, MG, PEG

Explore in 3D

2C78 \| pdb_00002c78	Download File View File

EF-Tu complexed with a GTP analog and the antibiotic pulvomycin

Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R.C., Nyborg, J., Nissen, P.

(2006) Biochemistry 45: 6846-6857

Released	2006-03-16
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Thermus thermophilus HB8
Macromolecule	ELONGATION FACTOR TU-A (protein)
Unique Ligands	GNP, MG, PUL