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Protein Structure Section

Introduction

The Protein Structure section of a Molecule Page gives potential PDB models for the protein sequence. A set of links to associated database records are displayed, as well as results from a Blast against the PDB sequences in the NCBI non-redundant protein database.

The database links are obtained from SwissProt records that are associated with the Molecule Page Protein. PDB and HSSP references are reported.

The Blast procedure uses the Blosum62 matrix with standard parameters, and reports the top 5 non-redundant protein sequences with an E-value of below 0.01. Each database record for a non-redundant protein is given, meaning that the number of records reported could be greater than five.

Database Link Categories

This Molecule's Sequence Is Identical To

The sequence in this database record is identical to that of the record used to define this Molecule Page protein. For a sequence to be in the "is identical to" category, it must be in the same species group as that of the defining database record, must have the same amino acid sequence as that of the defining sequence (allowing for a leading methionine), and there must be references that relate the record to the defining database record.

This Molecule's Sequence Is A Variant Of

The sequence in this database record is a variant of the record used to define this Molecule Page protein. For a sequence to be in the "is variant of" category, it must be in the same species group as that of the defining database record, must not be "is identical to", and must have a reference relating it to the "is defined by" record.

This Molecule's Sequence Is Related To

If the PDB record is for a different species than the one representing the Molecule Page protein, it falls in the "is related to" category.

This Molecule's Sequence Is Possibly Related To

These records are are related to any of the above record types by sequence identity, but not by any database reference. They also could be records that are related by database reference to another possibly related to sequence.

Database Link Fields

PDB ID

This is the ID of the PDB record, which is hyperlinked to the PDB web site.

Compound Name

This is the title used in the Fasta header in NCBI non-redundant protein Fasta file.

Species

The unique species name as given in the NCBI Taxonomy database. This field is hyperlinked to the NCBI Taxonomy browser, where one can see taxonomic hierarchy.

Additional Blast Fields

E-value

This is a statistical measure of the sequence similarity as reported by the Blast algorithm. In general, a lower E-value (i.e. one that is closer to zero) means a stronger similarity. This is hyperlinked to NCBI's Blast alignment viewer.

Score

This is a score of the sequence similarity as reported by the Blast algorithm. In general, a higher score means a stronger similarity.

Links

Hyperlinks to other databases with information on the structure.