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PDB (Protein Data Bank)

The PDB archive contains information about experimentally-determined structures of proteins,

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The Protein Data Bank (PDB) (http://www.pdb.org/) )archive is the single worldwiderepository of information about the 3D structures of large biological molecules, includingproteins and nucleic acids. These are the molecules of life that are found in all organismsincluding bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape ofa molecule helps to understand how it works. This knowledge can be used to help deduce astructure's role in human health and disease, and in drug development. The structures in thearchive range from tiny proteins and bits of DNA to complex molecular machines like theribosome.

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Method. It generates two mmCIF (Macromolecular Crystallographic File) where allinformations are merged.


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Ligand Depot : This server integrates informations releted to small molecules bound tomacromolecules including a graphical interface to search chemical structure.

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Summery Information of PDB Search

3ASW

Structural and biochemical characterization of ClfB:ligand interactions

Authors: Ganesh, V.K.ReleaseDate:

2011-05-04 Classification: Cell Adhesion

Experiment: X-RAY DIFFRACTION with resolution of 2.60

Compound:2 Polymers [Display Full Polymer Details|Display for AllResults]

Citation: Not Available.

Sample PDB Format

HEADER CELL ADHESION 22-DEC-10 3ASWTITLE STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF CLFB:LIGANDTITLE 2 INTERACTIONS

COMPND MOL_ID: 1;COMPND 2 MOLECULE: CLUMPING FACTOR B;

COMPND 3 CHAIN: A; ----------------------------PROTEIN B;

COMPND 6 ENGINEERED: YES;

COMPND 7 MUTATION: YES;SOURCE MOL_ID: 1;------------------------------------SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS;

SOURCE 13 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.

KEYWDS IGG LIKE, ADHESIN, CYTOKERATIN, CELL ADHESIONEXPDTA X-RAY DIFFRACTION

AUTHOR V.K.GANESHREVDAT 1 04-MAY-11 3ASW 0

JRNL AUTH

V.K.GANESH,E.M.BARBU,C.C.S.DEIVANAYAGAM,B.LE,A.ANDERSON,JRNL AUTH 2 Y.MATSUKA,S.L.LIN,T.J.FOSTER,SV.L.NARAYANA,M.HOOK

JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF

CLFB:LIGAND
http://www.pdb.org/pdb/explore/explore.do?structureId=3ASWhttp://www.pdb.org/pdb/explore/explore.do?structureId=3ASWhttp://www.pdb.org/pdb/explore/explore.do?structureId=3ASWhttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/explore/explore.do?structureId=3ASWhttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/results/results.do?outformat=&qrid=AE0623D3&tabtoshow=Currenthttp://www.pdb.org/pdb/explore/explore.do?structureId=3ASWhttp://www.pdb.org/pdb/explore/jmol.do?structureId=3ASWhttp://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3ASWhttp://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3ASWhttp://www.pdb.org/pdb/explore/explore.do?structureId=3ASW


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JRNL TITL 2 INTERACTIONSREMARK 2REMARK 2 RESOLUTION. 2.60 ANGSTROMS.REMARK 3

REMARK 3 REFINEMENT.REMARK 3 PROGRAM : REFMAC 5.2.0019

REMARK 3 ESU BASED ON FREE R VALUE (A):0.223REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A):

0.148REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2):

7.087 ----------------------------------------------------------

SEQRES 1 A 328 HIS HIS HIS HIS HIS HIS GLY SER GLY THR ASN VALASNSEQRES 2 A 328 ASP LYS VAL THR ALA SER ASN PHE LYS LEU GLU LYS

THR ------------------------------------------------------------ATOM 1 N GLY A 212 41.059 -8.999 -6.884 1.00 51.65

NATOM 2 CA GLY A 212 42.248 -8.275 -6.336 1.00 53.21C

ATOM 3 C GLY A 212 42.046 -7.660 -4.949 1.00 53.22C

1.00 29.95 OO -----------------------------------------------------------------

HETATM 2654 O HOH B 114 15.539 25.677 -18.531 1.00 36.53OHETATM 2655 O HOH B 135 18.524 26.554 -19.527 1.00 42.35

OMASTER 341 0 0 7 37 0 0 6 2653 2 0

28END

HEADER Types of proteinCOMPND Chemical compoundSOURCE Organism NameEXPDATA No of structure considered for NMR or other

experimentsAUTHOR Author of the workREVDAT Revised date

JRNL Journal InformationREMARK Information about paper publishedSEQRES Protein sequence using 3 letter amino acid codeFTNOTE Foot noteFORMUL Formula for compoundATOM Coordinate of sequence & name of atomCONECT Connectivity between the AtomsMODEL NMR data with model conformationsENDMDL End of model informationEND End of PDB File

(--------------------------)** Indication of Continuing.**


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pdb, bilogical data bases, bioinformatics data base

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