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Metalloprotein Database: Table Descriptions


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Protein Table
Field Name Description Possible Values
source_id unique identification number assigned to each coordinate file; provided by source  
source identifies from where coordinates were submitted pdb, tsri,
dep_date deposit date-identified the date the coordinates were deposited into the Protein Data Bank DD-MMM-YYYY format
rev_date revision date-identifies the date the coordinates were revised; this field may be null if there have been no revisions DD-MMM-YYYY format
expdata experimental data-identifies what method was used to prove the submitted coordinates xray, nmr, theoretical
description verbose description of the submitted structure; provided by the source  
resolution how close are atomic features distinguishable in the protein real #-supplies by coordinates
r_value how close is the fit of the electron density to an ideal model real #-supplies by corrdinates

Site Table    Site in this database means "metal" sites
Field Name Description Possible Values
site_id unique identifier that is derived from five different fields: source, source_id, metal name, metal chain and a generated sequence number all values are unique
num_ligands number of ligands-identifies the number of ligands in the metal site integer value
nlig_protein number of protein ligands-identifies the number of protein ligands contained in the metal site integer value
nlig_nucleic number of nucleic acids (DNA/RNA) within cut off distance-identifies the number of nucleic acids contained in the metal site integer value
nlig_metal number of metal within cut off distance-identifies the number of metal ligands contained in the metal site integer value
nlig_water number of water within cut off distance-identifies the number of water   contained in the metal site integer value

Ligand Table   
Field Name Description Possible Values
site_id unique identifier that is derived from five different fields: source, source_id, metal name, metal chain and a generated sequence number all values are unique
lig_type ligand type-identifies what type of ligand is being represented P=protein atom
N=nucleic acid
M=metal
W=water
A=anion
H=hetero
lig_chain pdb ligand chain-provided by the source provided by coordinates
lig_symbol pdb ligand symbol provided by coordinates
lig_seq pdb ligand sequence provided by coordinates
lig_atom pdb ligand atom provided by coordinates
metal_lig_dist metal ligand distance-calculated metal ligand distance from the coordinates real#-calculated from coordinate information



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Page maintained by Jesus M. Castagnetto (jesusmc@scripps.edu) - © The Scripps Research Institute.
Document: http://metallo.scripps.edu/sql_docs/table_descriptions.html
Last modified: Friday, Jan 17, 2003 at 13:51 (PST) - Last accessed: Thursday, Aug 28, 2008 at 16:40 (PDT)
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