3PN2A

Crystal structure of arabidopsis thaliana petide deformylase 1b (atpdf1b) (crystallized in peg-550-mme)
Total Genus 56
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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
56
sequence length
180
structure length
180
Chain Sequence
MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEA
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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 1B, chloroplastic
publication title Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.
pubmed doi rcsb
source organism Arabidopsis thaliana
total genus 56
structure length 180
sequence length 180
ec nomenclature ec 3.5.1.88: Peptide deformylase.
pdb deposition date 2010-11-18
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.45.10 Alpha Beta Alpha-Beta Complex Peptide Deformylase Peptide deformylase 3pn2A00
2AIEP 4EOXP 1DFFA 1Y6HA 5JF5A 1VEYA 3OCAA 1ICJA 5JF0A 3CMDA 2AI9A 3U7NA 4DR8A 5CWXA 3U04A 1ZXZA 2EW5A 3PN5A 1G2AA 1LRUA 3G6NA 1XENA 1LMHA 3CPMA 3SVJP 1G27A 3STRP 3FWXA 5CVPA 3PN4A 5CXJA 5E5DA 5JF2A 5CP0A 3PN3A 3UWBA 1RQCA 2AIAA 1SZZA 2EW7A 3O3JA 4NT8A 4DR9A 1BSKA 2W3UA 1JYMA 2AI8A 4AL3A 4JE8A 3E3UA 1BS8A 1BSJA 3PN6A 5I2BA 3G5PA 1LM4A 2AI7A 2EW6A 5CX0A 1V3YA 4AL2A 3U7KA 1BS7A 4E9BA 1WS1A 1N5NA 5KOBA 3M6QA 2DEFA 4JE7A 1BSZA 1LM6A 3UWAA 3M6RA 3G5KA 3QU1A 3L87A 3PN2A 1DEFA 3K6LA 1LMEA 3U7LA 3M6OA 4AZ4A 1S17A 1XEMA 4WXKA 2OKLA 1VEVA 5CPDA 5JF1A 5JF7A 1LQYA 5HGWA 5JF4A 1SV2A 1VEZA 5JEYA 1BS6A 1XEOA 5CWYA 2OS3A 1ZY0A 3U7MA 5J46A 5CY7A 5JF6A 5T8ZA 1LQWA 1BS4A 2OS1A 3M6PA 5JEZA 5CVQA 4E9AA 2W3TA 2KMNA 2OS0A 1Q1YA 5JF3A 1BS5A 1RL4A 1ZY1A 3SW8P 1WS0A 1IX1A 5JF8A 5CVKA 5CY8A 4JE6A 4WXLA 1LRYA 5JEXA
chains in the Genus database with same CATH superfamily
2AIEP 4EOXP 1DFFA 1Y6HA 5JF5A 1VEYA 3OCAA 1ICJA 5JF0A 3CMDA 2AI9A 3U7NA 4DR8A 5CWXA 3U04A 1ZXZA 2EW5A 3PN5A 1G2AA 1LRUA 3G6NA 1XENA 1LMHA 3CPMA 3SVJP 1G27A 3STRP 3FWXA 5CVPA 3PN4A 5CXJA 5E5DA 5JF2A 5CP0A 3PN3A 3UWBA 1RQCA 2AIAA 1SZZA 2EW7A 3O3JA 4NT8A 4DR9A 1BSKA 2W3UA 1JYMA 2AI8A 4AL3A 4JE8A 3E3UA 1BS8A 1BSJA 3PN6A 5I2BA 3G5PA 1LM4A 2AI7A 2EW6A 5CX0A 1V3YA 4AL2A 3U7KA 1BS7A 4E9BA 1WS1A 1N5NA 5KOBA 3M6QA 2DEFA 4JE7A 1BSZA 1LM6A 3UWAA 3M6RA 3G5KA 3QU1A 3L87A 3PN2A 1DEFA 3K6LA 1LMEA 3U7LA 3M6OA 4AZ4A 1S17A 1XEMA 4WXKA 2OKLA 1VEVA 5CPDA 5JF1A 5JF7A 1LQYA 5HGWA 5JF4A 1SV2A 1VEZA 5JEYA 1BS6A 1XEOA 5CWYA 2OS3A 1ZY0A 3U7MA 5J46A 5CY7A 5JF6A 5T8ZA 1LQWA 1BS4A 2OS1A 3M6PA 5JEZA 5CVQA 4E9AA 2W3TA 2KMNA 2OS0A 1Q1YA 5JF3A 1BS5A 1RL4A 1ZY1A 3SW8P 1WS0A 1IX1A 5JF8A 5CVKA 5CY8A 4JE6A 4WXLA 1LRYA 5JEXA
chains in the Genus database with same CATH topology
2AIEP 4EOXP 1DFFA 1Y6HA 5JF5A 1VEYA 3OCAA 1ICJA 5JF0A 3CMDA 2AI9A 3U7NA 4DR8A 5CWXA 3U04A 1ZXZA 2EW5A 3PN5A 1G2AA 1LRUA 3G6NA 1XENA 1LMHA 3CPMA 3SVJP 1G27A 3STRP 3FWXA 5CVPA 3PN4A 5CXJA 5E5DA 5JF2A 5CP0A 3PN3A 3UWBA 1RQCA 2AIAA 1SZZA 2EW7A 3O3JA 4NT8A 4DR9A 1BSKA 2W3UA 1JYMA 2AI8A 4AL3A 4JE8A 3E3UA 1BS8A 1BSJA 3PN6A 5I2BA 3G5PA 1LM4A 2AI7A 2EW6A 5CX0A 1V3YA 4AL2A 3U7KA 1BS7A 4E9BA 1WS1A 1N5NA 5KOBA 3M6QA 2DEFA 4JE7A 1BSZA 1LM6A 3UWAA 3M6RA 3G5KA 3QU1A 3L87A 3PN2A 1DEFA 3K6LA 1LMEA 3U7LA 3M6OA 4AZ4A 1S17A 1XEMA 4WXKA 2OKLA 1VEVA 5CPDA 5JF1A 5JF7A 1LQYA 5HGWA 5JF4A 1SV2A 1VEZA 5JEYA 1BS6A 1XEOA 5CWYA 2OS3A 1ZY0A 3U7MA 5J46A 5CY7A 5JF6A 5T8ZA 1LQWA 1BS4A 2OS1A 3M6PA 5JEZA 5CVQA 4E9AA 2W3TA 2KMNA 2OS0A 1Q1YA 5JF3A 1BS5A 1RL4A 1ZY1A 3SW8P 1WS0A 1IX1A 5JF8A 5CVKA 5CY8A 4JE6A 4WXLA 1LRYA 5JEXA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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