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Metalloprotein Database: Table Descriptions
| 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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