The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.
Total Genus |
55
|
Knots found |
|
sequence length |
194
|
structure length |
189
|
Chain Sequence |
GSDKIHHMLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV
|
The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Structure analysis of peptide deformylases from streptococcus pneumoniae,staphylococcus aureus, thermotoga maritima, and pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
pubmed doi rcsb |
| molecule tags |
Hydrolase
|
| source organism |
Staphylococcus aureus
|
| molecule keywords |
peptide deformylase PDF1
|
| total genus |
55
|
| structure length |
189
|
| sequence length |
194
|
| chains with identical sequence |
B
|
| other databases |
 KnotProt 2.0: S -31
|
| ec nomenclature |
ec
3.5.1.88: Peptide deformylase. |
| pdb deposition date | 2002-04-30 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF01327 | Pep_deformylase | Polypeptide deformylase |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Alpha Beta | Alpha-Beta Complex | Peptide Deformylase | Peptide deformylase |
#chains in the Genus database with same CATH superfamily 4WXL A; 4AL2 A; 4DR8 A; 3L87 A; 5JF4 A; 2AI8 A; 2AI7 A; 5JEZ A; 4EOX P; 1IX1 A; 3PN6 A; 3PN4 A; 3M6P A; 1VEV A; 1SV2 A; 1G2A A; 5CWX A; 1BSZ A; 4WXK A; 2EW5 A; 1LQY A; 1Q1Y A; 1RL4 A; 2OKL A; 5T8Z A; 5KOB A; 3SVJ P; 5JEY A; 4NT8 A; 1WS0 A; 3QU1 A; 1V3Y A; 1LME A; 2EW7 A; 1SZZ A; 5JF2 A; 2KMN A; 4AZ4 A; 1ZY1 A; 5CVQ A; 2W3T A; 1LQW A; 3SW8 P; 1N5N A; 2OS3 A; 1S17 A; 5CY8 A; 3UWA A; 1LRY A; 5JF7 A; 5JF6 A; 2OS0 A; 1RQC A; 1LM6 A; 5CVK A; 1XEO A; 1XEN A; 3PN5 A; 5CXJ A; 1LRU A; 2AIE P; 4E9A A; 3U7N A; 5JF3 A; 4E9B A; 3PN3 A; 2EW6 A; 3FWX A; 3E3U A; 5CPD A; 1DFF A; 3U7L A; 1BS4 A; 3PN2 A; 1Y6H A; 1JYM A; 1G27 A; 2AIA A; 3M6R A; 5J46 A; 5JF5 A; 5JF0 A; 1BS6 A; 1XEM A; 2OS1 A; 3OCA A; 5E5D A; 1DEF A; 3U04 A; 3G5P A; 1VEY A; 3K6L A; 1LM4 A; 4JE6 A; 3UWB A; 4DR9 A; 1BS8 A; 1BS7 A; 4JE8 A; 1BS5 A; 3O3J A; 1LMH A; 3M6Q A; 5JF8 A; 5JEX A; 5JF1 A; 3U7K A; 2AI9 A; 5CX0 A; 3CMD A; 1ZY0 A; 5CP0 A; 3M6O A; 5CVP A; 5HGW A; 1ZXZ A; 4JE7 A; 2DEF A; 3STR P; 1VEZ A; 5I2B A; 1WS1 A; 3G5K A; 2W3U A; 4AL3 A; 5CWY A; 3G6N A; 3CPM A; 1BSK A; 1ICJ A; 5CY7 A; 3U7M A; 1BSJ A; #chains in the Genus database with same CATH topology 4WXL A; 4AL2 A; 4DR8 A; 3L87 A; 5JF4 A; 2AI8 A; 2AI7 A; 5JEZ A; 4EOX P; 1IX1 A; 3PN6 A; 3PN4 A; 3M6P A; 1VEV A; 1SV2 A; 1G2A A; 5CWX A; 1BSZ A; 4WXK A; 2EW5 A; 1LQY A; 1Q1Y A; 1RL4 A; 2OKL A; 5T8Z A; 5KOB A; 3SVJ P; 5JEY A; 4NT8 A; 1WS0 A; 3QU1 A; 1V3Y A; 1LME A; 2EW7 A; 1SZZ A; 5JF2 A; 2KMN A; 4AZ4 A; 1ZY1 A; 5CVQ A; 2W3T A; 1LQW A; 3SW8 P; 1N5N A; 2OS3 A; 1S17 A; 5CY8 A; 3UWA A; 1LRY A; 5JF7 A; 5JF6 A; 2OS0 A; 1RQC A; 1LM6 A; 5CVK A; 1XEO A; 1XEN A; 3PN5 A; 5CXJ A; 1LRU A; 2AIE P; 4E9A A; 3U7N A; 5JF3 A; 4E9B A; 3PN3 A; 2EW6 A; 3FWX A; 3E3U A; 5CPD A; 1DFF A; 3U7L A; 1BS4 A; 3PN2 A; 1Y6H A; 1JYM A; 1G27 A; 2AIA A; 3M6R A; 5J46 A; 5JF5 A; 5JF0 A; 1BS6 A; 1XEM A; 2OS1 A; 3OCA A; 5E5D A; 1DEF A; 3U04 A; 3G5P A; 1VEY A; 3K6L A; 1LM4 A; 4JE6 A; 3UWB A; 4DR9 A; 1BS8 A; 1BS7 A; 4JE8 A; 1BS5 A; 3O3J A; 1LMH A; 3M6Q A; 5JF8 A; 5JEX A; 5JF1 A; 3U7K A; 2AI9 A; 5CX0 A; 3CMD A; 1ZY0 A; 5CP0 A; 3M6O A; 5CVP A; 5HGW A; 1ZXZ A; 4JE7 A; 2DEF A; 3STR P; 1VEZ A; 5I2B A; 1WS1 A; 3G5K A; 2W3U A; 4AL3 A; 5CWY A; 3G6N A; 3CPM A; 1BSK A; 1ICJ A; 5CY7 A; 3U7M A; 1BSJ A; #chains in the Genus database with same CATH homology 4WXL A; 4AL2 A; 4DR8 A; 3L87 A; 5JF4 A; 2AI8 A; 2AI7 A; 5JEZ A; 4EOX P; 1IX1 A; 3PN6 A; 3PN4 A; 3M6P A; 1VEV A; 1SV2 A; 1G2A A; 5CWX A; 1BSZ A; 4WXK A; 2EW5 A; 1LQY A; 1Q1Y A; 1RL4 A; 2OKL A; 5T8Z A; 5KOB A; 3SVJ P; 5JEY A; 4NT8 A; 1WS0 A; 3QU1 A; 1V3Y A; 1LME A; 2EW7 A; 1SZZ A; 5JF2 A; 2KMN A; 4AZ4 A; 1ZY1 A; 5CVQ A; 2W3T A; 1LQW A; 3SW8 P; 1N5N A; 2OS3 A; 1S17 A; 5CY8 A; 3UWA A; 1LRY A; 5JF7 A; 5JF6 A; 2OS0 A; 1RQC A; 1LM6 A; 5CVK A; 1XEO A; 1XEN A; 3PN5 A; 5CXJ A; 1LRU A; 2AIE P; 4E9A A; 3U7N A; 5JF3 A; 4E9B A; 3PN3 A; 2EW6 A; 3FWX A; 3E3U A; 5CPD A; 1DFF A; 3U7L A; 1BS4 A; 3PN2 A; 1Y6H A; 1JYM A; 1G27 A; 2AIA A; 3M6R A; 5J46 A; 5JF5 A; 5JF0 A; 1BS6 A; 1XEM A; 2OS1 A; 3OCA A; 5E5D A; 1DEF A; 3U04 A; 3G5P A; 1VEY A; 3K6L A; 1LM4 A; 4JE6 A; 3UWB A; 4DR9 A; 1BS8 A; 1BS7 A; 4JE8 A; 1BS5 A; 3O3J A; 1LMH A; 3M6Q A; 5JF8 A; 5JEX A; 5JF1 A; 3U7K A; 2AI9 A; 5CX0 A; 3CMD A; 1ZY0 A; 5CP0 A; 3M6O A; 5CVP A; 5HGW A; 1ZXZ A; 4JE7 A; 2DEF A; 3STR P; 1VEZ A; 5I2B A; 1WS1 A; 3G5K A; 2W3U A; 4AL3 A; 5CWY A; 3G6N A; 3CPM A; 1BSK A; 1ICJ A; 5CY7 A; 3U7M A; 1BSJ A;
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