http://www.wwpdb.org/
INTRODUCTION
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| http://www.rcsb.org/pdb/explore/images.do?structureId=6PAX |
The PDB is the Protein Data Bank, a single worlwide repository for 3D structural data of biological molecules. A PDB is a file, typically with a "pdb" file extension, contains 3D structural data of a particular biological molecule. In short, a PDB file is broken into two sections: (i) a header that contains much background information on the molecule in question such as authors and experimental conditions, (ii) 3D coordinate data that contain the vital experimental data in the form of 3D cartesian coordinates, B-factors, atom information, and more.
The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB.
The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education. Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses. However, it can be a challenge to find the information that you need, since the PDB archives so many different structures. You will often find multiple structures for a given molecule, or partial structures, or structures that have been modified or inactivated from their native form.
INTRODUCTION OF RASMOL
http://www.google.com.my/imgresum=1&hl=ms&sa=N&tbm=isch&tbnid=GhR5jNOSXfXs_M:&imgrefurl=http://www.umass.edu/microbio/rasmol/index2.ht
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK.
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo Research and Development, Greenford, UK.
RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files. If connectivity information and/or secondary structure information is not contained in the file this is calculated automatically. The loaded molecule may be shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. Atoms may also be labelled with arbitrary text strings.
RasMol can also create a script file containing the commands required to regenerate the current image. Finally the rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.
RasMol will run on a wide range of architectures and systems including SGI, sun4, sun3, sun386i, DEC, HP and E&S workstations, IBM RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame buffer (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory rendering (via the XInput and MIT-SHM extensions) if available.
TRYPSIN
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| SYNTHETIC CONSTRUCT |
Molecular name : PANCREATIC TRYPSIN INHIBITOR PRECURSOR
Classification : Proteinase inhibitor (trypsin)
Data Base Code : 6PTI
Number of Chain : 2
Number of Group : 57 (74)
Number of Atom : 458 (78)
Number of Bond : 476
Polymer : 2
Type : Protein
Length : 58
Chains : I
JOURNAL : (1983) Acta Crystallogr. , Sect. B 39 : 480
Lex A
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| NORWALK VIRUS |
Classification : Viral Protein
Data Base Code : 3Q6R
Number of Chains : 6
Number of Groups : 620 (990)
Number of Atom : 4826 (1067)
Number of Bond : 5047
Polymer : 1
Length : 319
Chains : A, B
JOURNAL : (2011) J. Virol. 85 : 6687 - 6701
Htr A
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| SYNTHETIC CONSTRUCT |
Classification : RNA
Data Base Code : 2K96
Number of Chains : 20
Number of Group : 940
Number of Atoms : 29900
Number of Bonds : 32200
Polymer : 1
Length : 47
Chains : A
JOURNAL : (2008) J. Mol. Biol. 384 : 1249 - 1261
Molecular Name
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Type
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|---|---|
Capsid Protein
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Protein
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TELOMERASE RNA P2B - P3 PSEUDOKNOT
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rna
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PROTEIN (ClpA chaperone)
ClpA is a protein that we can classified it under Hydrolase group.The ClpA type can be found at Escherichia coli (E.coli). ClpA consists of three functional domains that are an N-terminal domain and two ATPase domains,D1 and D2.
The N-domain is attached to D1 by a mobile linker and is made up of two tightly bound, identically folded alpha-helical bundles related by pseudo 2-fold symmetry.
ClpB STRUCTURE
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ClpB is essential proteins of the heat-shock response and belong to the class 1 family of Clp. Member of this family form large ring structures and contain two AAA+ modules, which consist of a RecA-like nucleotide-binding domain (NBD) and an α-helical domain. Furthermore, ClpB has a longer middle region, the ClpB linker, which is essential for chaperone activity. Unlike other Clp protein, however, ClpB neither associates with a cellular protease nor directs the degradation of its substrate proteins. Rather, ClpB is a bona fidemolecular chaperone, which has the remarkable ability to rescue proteins from an aggregated state. The full recovery of these proteins requires the assistance of the cognate DnaK/Hsp70 chaperone system. The mechanism of this “bi-chaperone” network, however, remains elusive. Here we review the current understanding of the structure–function relationship of the ClpB molecular chaperone and its role in protein disaggregation.
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