Schema for PDB Structures - Protein Data Bank (PDB) Sequence Matches |
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Database: wuhCor1 Primary Table: pdb Data last updated: 2023-11-23
Big Bed File Download: /gbdb/wuhCor1/bbi/pdb.bb
Item Count: 3,790
The data is stored in the binary BigBed format.
Format description: Browser Extensible Data
| field | example | description |
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| chrom | NC_045512v2 | Reference sequence chromosome or scaffold | | chromStart | 19617 | Start position in chromosome | | chromEnd | 20655 | End position in chromosome | | name | 2h85 | Name of item. | | score | 764 | Score (0-1000) | | strand | + | + or - for strand | | thickStart | 19617 | Start of where display should be thick (start codon) | | thickEnd | 20655 | End of where display should be thick (stop codon) | | reserved | 0 | Used as itemRgb as of 2004-11-22 | | blockCount | 1 | Number of blocks | | blockSizes | 1038, | Comma separated list of block sizes | | chromStarts | 0, | Start positions relative to chromStart |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
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| NC_045512v2 | 19617 | 20655 | 2h85 | 764 | + | 19617 | 20655 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7rb2 | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7rb0 | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7n83 | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7n7y | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7n7w | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7n7u | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7n7r | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7me0 | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
| NC_045512v2 | 19620 | 20658 | 7kf4 | 1000 | + | 19620 | 20658 | 0 | 1 | 1038, | 0, |
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PDB Structures (pdb) Track Description
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Description
This track shows alignments of sequences with known protein structures in the
Protein Data Bank (PDB).
The PDB protein sequence has to match the genome over at least 80% of its length,
so somewhat similar sequences, e.g. from the SARS 2003 outbreak, are also shown.
Display Conventions and Configuration
Genomic locations of PDB matches are labeled with the accession number.
A click on them shows a standard feature detail page with the PDB page integrated into it.
The protein structure is shown on the PDB page.
Methods
PDB sequences were downloaded from the
PDB website and aligned
with BLAT. Only alignments with a minimum identity of 80%
that span at least 80% of the query sequence were kept.
References
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE.
The Protein Data Bank.
Nucleic Acids Res. 2000 Jan 1;28(1):235-42.
PMID: 10592235; PMC: PMC102472
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