The Jena3D Viewer (Jena3D) is a web-based interactive viewer for three-dimensional biopolymer structures.

Jena3D provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).
In addition, local structure files can be viewed.

Jena3D is based on Jmol, an open source Java applet.

Jena3D visualizes not only information included in the PDB files but also SCOP, CATH and Pfam domains, SAPs(SNPs), PROSITE motifs and the exon structure mapped onto proteins.

Jena3D is closely linked to the Jena Library of Biological Macromolecules (JenaLib).

The Jmol Java applet that is the basis of Jena3D is available in two versions:

1. The unsigned applet is the default that is used from QuickSearch result links (see below) and crosslinks from the JenaLib.

   It is not able to read or write any files on your computer.

2. The signed applet can be selected before loading a structure into Jena3D.
   use signed Jmol applet  use unsigned Jmol applet
   It can read or write files on your computer. This enables to export images in different formats (e.g.: PNG, JPEG, POVRay).

   But this is a potential security risk!. Depending on the configuration of your computer it might be possible that the applet for example reads or replaces system or confidential files.
   So if you don't trust us or the Jmol developers don't use the signed applet!

   Because of the higher security risk the browser will ask you if you really want to trust the signed applet before it is started. If you say "no" the applet will only be allowed to do the same things as the unsigned applet.

The Jena3D interface works fully both with the unsigned and the signed applet.

For the upload function (described in the Loading 3D Structures section below) the file is not read directly by the applet. Instead it is read by the browser and sent to the Jena3D server. The applet then reads the file from the server. This way you have full control over the files that are read on your computer by Jena3D. This procedure is also used because the Jena3D interface is specifically built for each structure that is loaded.

So only if you need the extended export possibilities of Jmol (see the Export section below) the signed applet is required.

[sorry, this part is not available yet]

[sorry, this part is not available yet]

[sorry, this part is not available yet]

[sorry, this part is not available yet]

There are four ways to load a 3D structure into Jena3D:

1. Enter direcly a structure identifier from the Protein Data Bank (PDB code) or the Nucleic Acid Database (NDB code) into the QuickSearch input field.

   QuickSearch:

2. Enter a UniProt / PROSITE id or accession number or search term(s) into the QuickSearch input field.

   QuickSearch:

   Select a structure from the search results and click onto one of the Jena3D links 3D3D in the result list.

   1MMZ	3D3D	(3)	CRYSTAL STRUCTURE OF GALACTOSE MUTAROTASE FROM LACTOCOCCUS LACTIS COMPLEXED WITH L-ARABINOSE

   	Header Line:	isomerase
   	Hetero Full Name:	beta-l-arabinose
   	Structure Title:	crystal structure of galactose mutarotase from lactococcus lactis complexed with l-arabinose

3. Select a structure file on your computer that should be uploaded into Jena3D.

   Upload:

   You can upload any molecular structure file format that is recognized by Jmol,
   e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
   (also compressed with 'gzip', see the Jmol documentation for a complete list)
4. By default the asymmetric unit file of a PDB entry is loaded into Jena3D.
   In the menu at the top of the interface you can choose between all available asymmetric and biological unit files for a specific PDB entry.

   4OTB

   Asym. UnitInfo Asym.Unit (107 KB)Biol.Unit 1 (56 KB)Biol.Unit 2 (53 KB)Biol.Unit 3 (53 KB)Biol.Unit 4 (53 KB)Biol.Unit 5 (52 KB)Biol.Unit 6 (52 KB)

   Title	:	4-OXALOCROTONATE TAUTOMERASE OBSERVED AS AN OCTODECAMER, RHOMBOHEDRAL CRYSTAL FORM
   Authors	:	A. B. Taylor, C. P. Whitman, M. L. Hackert
   Date	:	15 Oct 98  (Deposition) - 01 Aug 01  (Release) - 01 Aug 01  (Revision)
   Method	:	X-RAY DIFFRACTION
   Resolution	:	2.50
   Chains	:	Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,_# Biol. Unit 1:  A,B,_#  (3x) Biol. Unit 2:  C,D  (3x) Biol. Unit 3:  E,F  (3x) Biol. Unit 4:  G,H  (3x) Biol. Unit 5:  I,J  (3x) Biol. Unit 6:  K,L  (3x) ( #:   chains that contain no standard or modified protein/DNA/RNA residue)
   Reference	:	A. B. Taylor Native And Inhibitor Complex Structures Of 4-Oxalocrotonate Tautomerase From Pseudomonas Putida Mt-2 (University Of Texas At Austin-136 Pages) Thesis 1998 (for further references see the PDB file header)

       [ close entry info ] Biological units are only available for crystallographic structures. For NMR structures the "NMR structure *" file (which is provided by the wwPDB as biological unit file) is identical with the "NMR structure" file.

   1JM7

   NMR StructureInfo NMR Structure (745 KB)NMR Structure * (743 KB)

   Title	:	SOLUTION STRUCTURE OF THE BRCA1/BARD1 RING-DOMAIN HETERODIMER
   Authors	:	P. S. Brzovic, P. Rajagopal, D. W. Hoyt, M. -C. King, R. E. Klevit
   Date	:	17 Jul 01  (Deposition) - 03 Oct 01  (Release) - 01 Apr 03  (Revision)
   Method	:	NMR, 14 STRUCTURES
   Resolution	:	NOT APPLICABLE
   Chains	:	NMR Structure  :  A,B  (14  structures) NMR Structure *:  A,B  (14 structures)
   Reference	:	P. S. Brzovic, P. Rajagopal, D. W. Hoyt, M. C. King, R. E. Klevit Structure Of A Brca1-Bard1 Heterodimeric Ring-Ring Complex. Nat. Struct. Biol. V. 8 833 2001 (for further references see the PDB file header)

       [ close entry info ]

[sorry, this part is not available yet]

[sorry, this part is not available yet]

Detailed information on the QuickSearch option is available on the JenaLib QuickSearch Help page.
A quick introduction is presented in the Loading 3D Structures section above.

[sorry, this part is not available yet]

[sorry, this part is not available yet]