1LM4A

Structure of peptide deformylase from staphylococcus aureus at 1.45 a
Total Genus 55
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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
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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.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Hydrolase
molecule keywords peptide deformylase PDF1
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
source organism Staphylococcus aureus
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

pfam database annotations

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
ClassArchitectureTopologyHomologyDomain
3.90.45.10 Alpha Beta Alpha-Beta Complex Peptide Deformylase Peptide deformylase 1lm4A00
5CWXA 3M6RA 5T8ZA 1LQYA 1XEMA 4JE7A 2W3UA 1IX1A 4NT8A 1BSZA 3K6LA 5I2BA 3U7MA 1RL4A 2OS1A 3SW8P 1Y6HA 5JF8A 1VEZA 5JF0A 1WS1A 1XENA 2EW6A 3PN6A 1ZY1A 5JF1A 5KOBA 4E9BA 5JEZA 1G27A 2W3TA 4EOXP 1VEYA 4JE6A 1LMEA 3CPMA 5E5DA 1BS7A 1LRUA 5CY8A 1VEVA 4E9AA 5CVPA 1WS0A 1BS8A 2EW7A 3U7KA 2AIAA 1SZZA 3SVJP 5J46A 5JF5A 3U7LA 1S17A 3M6QA 1LMHA 5HGWA 5CPDA 3O3JA 1LM6A 1LM4A 2AI7A 1ZXZA 2AIEP 3UWBA 5JEYA 5JF2A 1G2AA 5CXJA 1DFFA 3U7NA 4WXLA 3U04A 3G6NA 5CVKA 1LQWA 4JE8A 1BSKA 1SV2A 3FWXA 4WXKA 1ZY0A 4AL2A 4AZ4A 2AI8A 1DEFA 3G5PA 1BS5A 3M6OA 3STRP 2AI9A 1LRYA 1BS6A 3PN5A 5JF4A 3PN4A 3OCAA 5CP0A 1BS4A 1ICJA 4DR8A 5CVQA 2OS0A 4DR9A 2EW5A 5CWYA 2DEFA 1Q1YA 2OKLA 3L87A 2KMNA 1BSJA 5CX0A 3QU1A 1RQCA 5JEXA 3CMDA 5JF6A 3E3UA 3PN2A 3G5KA 1JYMA 1V3YA 5JF3A 1XEOA 1N5NA 3M6PA 5JF7A 4AL3A 2OS3A 3PN3A 5CY7A 3UWAA
chains in the Genus database with same CATH superfamily
5CWXA 3M6RA 5T8ZA 1LQYA 1XEMA 4JE7A 2W3UA 1IX1A 4NT8A 1BSZA 3K6LA 5I2BA 3U7MA 1RL4A 2OS1A 3SW8P 1Y6HA 5JF8A 1VEZA 5JF0A 1WS1A 1XENA 2EW6A 3PN6A 1ZY1A 5JF1A 5KOBA 4E9BA 5JEZA 1G27A 2W3TA 4EOXP 1VEYA 4JE6A 1LMEA 3CPMA 5E5DA 1BS7A 1LRUA 5CY8A 1VEVA 4E9AA 5CVPA 1WS0A 1BS8A 2EW7A 3U7KA 2AIAA 1SZZA 3SVJP 5J46A 5JF5A 3U7LA 1S17A 3M6QA 1LMHA 5HGWA 5CPDA 3O3JA 1LM6A 1LM4A 2AI7A 1ZXZA 2AIEP 3UWBA 5JEYA 5JF2A 1G2AA 5CXJA 1DFFA 3U7NA 4WXLA 3U04A 3G6NA 5CVKA 1LQWA 4JE8A 1BSKA 1SV2A 3FWXA 4WXKA 1ZY0A 4AL2A 4AZ4A 2AI8A 1DEFA 3G5PA 1BS5A 3M6OA 3STRP 2AI9A 1LRYA 1BS6A 3PN5A 5JF4A 3PN4A 3OCAA 5CP0A 1BS4A 1ICJA 4DR8A 5CVQA 2OS0A 4DR9A 2EW5A 5CWYA 2DEFA 1Q1YA 2OKLA 3L87A 2KMNA 1BSJA 5CX0A 3QU1A 1RQCA 5JEXA 3CMDA 5JF6A 3E3UA 3PN2A 3G5KA 1JYMA 1V3YA 5JF3A 1XEOA 1N5NA 3M6PA 5JF7A 4AL3A 2OS3A 3PN3A 5CY7A 3UWAA
chains in the Genus database with same CATH topology
5CWXA 3M6RA 5T8ZA 1LQYA 1XEMA 4JE7A 2W3UA 1IX1A 4NT8A 1BSZA 3K6LA 5I2BA 3U7MA 1RL4A 2OS1A 3SW8P 1Y6HA 5JF8A 1VEZA 5JF0A 1WS1A 1XENA 2EW6A 3PN6A 1ZY1A 5JF1A 5KOBA 4E9BA 5JEZA 1G27A 2W3TA 4EOXP 1VEYA 4JE6A 1LMEA 3CPMA 5E5DA 1BS7A 1LRUA 5CY8A 1VEVA 4E9AA 5CVPA 1WS0A 1BS8A 2EW7A 3U7KA 2AIAA 1SZZA 3SVJP 5J46A 5JF5A 3U7LA 1S17A 3M6QA 1LMHA 5HGWA 5CPDA 3O3JA 1LM6A 1LM4A 2AI7A 1ZXZA 2AIEP 3UWBA 5JEYA 5JF2A 1G2AA 5CXJA 1DFFA 3U7NA 4WXLA 3U04A 3G6NA 5CVKA 1LQWA 4JE8A 1BSKA 1SV2A 3FWXA 4WXKA 1ZY0A 4AL2A 4AZ4A 2AI8A 1DEFA 3G5PA 1BS5A 3M6OA 3STRP 2AI9A 1LRYA 1BS6A 3PN5A 5JF4A 3PN4A 3OCAA 5CP0A 1BS4A 1ICJA 4DR8A 5CVQA 2OS0A 4DR9A 2EW5A 5CWYA 2DEFA 1Q1YA 2OKLA 3L87A 2KMNA 1BSJA 5CX0A 3QU1A 1RQCA 5JEXA 3CMDA 5JF6A 3E3UA 3PN2A 3G5KA 1JYMA 1V3YA 5JF3A 1XEOA 1N5NA 3M6PA 5JF7A 4AL3A 2OS3A 3PN3A 5CY7A 3UWAA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5CWX A;  3M6R A;  5T8Z A;  1LQY A;  1XEM A;  4JE7 A;  2W3U A;  1IX1 A;  4NT8 A;  1BSZ A;  3K6L A;  5I2B A;  3U7M A;  1RL4 A;  2OS1 A;  3SW8 P;  1Y6H A;  5JF8 A;  1VEZ A;  5JF0 A;  1WS1 A;  1XEN A;  2EW6 A;  3PN6 A;  1ZY1 A;  5JF1 A;  5KOB A;  4E9B A;  5JEZ A;  1G27 A;  2W3T A;  4EOX P;  1VEY A;  4JE6 A;  1LME A;  3CPM A;  5E5D A;  1BS7 A;  1LRU A;  5CY8 A;  1VEV A;  4E9A A;  5CVP A;  1WS0 A;  1BS8 A;  2EW7 A;  3U7K A;  2AIA A;  1SZZ A;  3SVJ P;  5J46 A;  5JF5 A;  3U7L A;  1S17 A;  3M6Q A;  1LMH A;  5HGW A;  5CPD A;  3O3J A;  1LM6 A;  1LM4 A;  2AI7 A;  1ZXZ A;  2AIE P;  3UWB A;  5JEY A;  5JF2 A;  1G2A A;  5CXJ A;  1DFF A;  3U7N A;  4WXL A;  3U04 A;  3G6N A;  5CVK A;  1LQW A;  4JE8 A;  1BSK A;  1SV2 A;  3FWX A;  4WXK A;  1ZY0 A;  4AL2 A;  4AZ4 A;  2AI8 A;  1DEF A;  3G5P A;  1BS5 A;  3M6O A;  3STR P;  2AI9 A;  1LRY A;  1BS6 A;  3PN5 A;  5JF4 A;  3PN4 A;  3OCA A;  5CP0 A;  1BS4 A;  1ICJ A;  4DR8 A;  5CVQ A;  2OS0 A;  4DR9 A;  2EW5 A;  5CWY A;  2DEF A;  1Q1Y A;  2OKL A;  3L87 A;  2KMN A;  1BSJ A;  5CX0 A;  3QU1 A;  1RQC A;  5JEX A;  3CMD A;  5JF6 A;  3E3U A;  3PN2 A;  3G5K A;  1JYM A;  1V3Y A;  5JF3 A;  1XEO A;  1N5N A;  3M6P A;  5JF7 A;  4AL3 A;  2OS3 A;  3PN3 A;  5CY7 A;  3UWA A; 
#chains in the Genus database with same CATH topology
 5CWX A;  3M6R A;  5T8Z A;  1LQY A;  1XEM A;  4JE7 A;  2W3U A;  1IX1 A;  4NT8 A;  1BSZ A;  3K6L A;  5I2B A;  3U7M A;  1RL4 A;  2OS1 A;  3SW8 P;  1Y6H A;  5JF8 A;  1VEZ A;  5JF0 A;  1WS1 A;  1XEN A;  2EW6 A;  3PN6 A;  1ZY1 A;  5JF1 A;  5KOB A;  4E9B A;  5JEZ A;  1G27 A;  2W3T A;  4EOX P;  1VEY A;  4JE6 A;  1LME A;  3CPM A;  5E5D A;  1BS7 A;  1LRU A;  5CY8 A;  1VEV A;  4E9A A;  5CVP A;  1WS0 A;  1BS8 A;  2EW7 A;  3U7K A;  2AIA A;  1SZZ A;  3SVJ P;  5J46 A;  5JF5 A;  3U7L A;  1S17 A;  3M6Q A;  1LMH A;  5HGW A;  5CPD A;  3O3J A;  1LM6 A;  1LM4 A;  2AI7 A;  1ZXZ A;  2AIE P;  3UWB A;  5JEY A;  5JF2 A;  1G2A A;  5CXJ A;  1DFF A;  3U7N A;  4WXL A;  3U04 A;  3G6N A;  5CVK A;  1LQW A;  4JE8 A;  1BSK A;  1SV2 A;  3FWX A;  4WXK A;  1ZY0 A;  4AL2 A;  4AZ4 A;  2AI8 A;  1DEF A;  3G5P A;  1BS5 A;  3M6O A;  3STR P;  2AI9 A;  1LRY A;  1BS6 A;  3PN5 A;  5JF4 A;  3PN4 A;  3OCA A;  5CP0 A;  1BS4 A;  1ICJ A;  4DR8 A;  5CVQ A;  2OS0 A;  4DR9 A;  2EW5 A;  5CWY A;  2DEF A;  1Q1Y A;  2OKL A;  3L87 A;  2KMN A;  1BSJ A;  5CX0 A;  3QU1 A;  1RQC A;  5JEX A;  3CMD A;  5JF6 A;  3E3U A;  3PN2 A;  3G5K A;  1JYM A;  1V3Y A;  5JF3 A;  1XEO A;  1N5N A;  3M6P A;  5JF7 A;  4AL3 A;  2OS3 A;  3PN3 A;  5CY7 A;  3UWA A; 
#chains in the Genus database with same CATH homology
 5CWX A;  3M6R A;  5T8Z A;  1LQY A;  1XEM A;  4JE7 A;  2W3U A;  1IX1 A;  4NT8 A;  1BSZ A;  3K6L A;  5I2B A;  3U7M A;  1RL4 A;  2OS1 A;  3SW8 P;  1Y6H A;  5JF8 A;  1VEZ A;  5JF0 A;  1WS1 A;  1XEN A;  2EW6 A;  3PN6 A;  1ZY1 A;  5JF1 A;  5KOB A;  4E9B A;  5JEZ A;  1G27 A;  2W3T A;  4EOX P;  1VEY A;  4JE6 A;  1LME A;  3CPM A;  5E5D A;  1BS7 A;  1LRU A;  5CY8 A;  1VEV A;  4E9A A;  5CVP A;  1WS0 A;  1BS8 A;  2EW7 A;  3U7K A;  2AIA A;  1SZZ A;  3SVJ P;  5J46 A;  5JF5 A;  3U7L A;  1S17 A;  3M6Q A;  1LMH A;  5HGW A;  5CPD A;  3O3J A;  1LM6 A;  1LM4 A;  2AI7 A;  1ZXZ A;  2AIE P;  3UWB A;  5JEY A;  5JF2 A;  1G2A A;  5CXJ A;  1DFF A;  3U7N A;  4WXL A;  3U04 A;  3G6N A;  5CVK A;  1LQW A;  4JE8 A;  1BSK A;  1SV2 A;  3FWX A;  4WXK A;  1ZY0 A;  4AL2 A;  4AZ4 A;  2AI8 A;  1DEF A;  3G5P A;  1BS5 A;  3M6O A;  3STR P;  2AI9 A;  1LRY A;  1BS6 A;  3PN5 A;  5JF4 A;  3PN4 A;  3OCA A;  5CP0 A;  1BS4 A;  1ICJ A;  4DR8 A;  5CVQ A;  2OS0 A;  4DR9 A;  2EW5 A;  5CWY A;  2DEF A;  1Q1Y A;  2OKL A;  3L87 A;  2KMN A;  1BSJ A;  5CX0 A;  3QU1 A;  1RQC A;  5JEX A;  3CMD A;  5JF6 A;  3E3U A;  3PN2 A;  3G5K A;  1JYM A;  1V3Y A;  5JF3 A;  1XEO A;  1N5N A;  3M6P A;  5JF7 A;  4AL3 A;  2OS3 A;  3PN3 A;  5CY7 A;  3UWA A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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