1ZY0A

X-ray structure of peptide deformylase from arabidopsis thaliana (atpdf1a); crystals grown in peg-6000
Total Genus 46

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
46
sequence length
191
structure length
191
Chain Sequence
DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSH

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
3H2 (52-55)EMPTYTI2 (111-114)TIV1 (8-11)TIV2 (22-25)TIV4 (24-27)AH1 (29-44)TI1 (25-28)S4 (114-133)S2 (61-66)S1 (49-51)O1 (57-59)S3 (87-111)AH4 (145-158)AH2 (68-72)AH3 (76-82)S6 (173-174)TIV9 (168-171)3H3 (163-165)TI4 (177-180)3H4 (175-177)TII1 (183-186)3H1 (12-14)S5 (137-144)TI3 (133-136)Updating...
connected with : NaN
molecule tags Hydrolase
source organism Arabidopsis thaliana
publication title The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms
pubmed doi rcsb
molecule keywords Peptide deformylase, mitochondrial
total genus 46
structure length 191
sequence length 191
chains with identical sequence B
ec nomenclature ec 3.5.1.88: Peptide deformylase.
pdb deposition date 2005-06-09

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 1zy0A00
5E5DA 1SV2A 1LMHA 4WXKA 1BS5A 3OCAA 1SZZA 3UWAA 3PN6A 3PN3A 2OS0A 3CMDA 1VEZA 2AI7A 4AL2A 1BSZA 2OS1A 5CWXA 2EW6A 4AL3A 5JF4A 1LM4A 3STRP 1LRUA 1BS7A 1BSKA 1BS6A 5CVPA 3PN4A 1XEMA 1LQWA 1BS4A 2AI9A 1IX1A 3QU1A 3M6QA 3SW8P 2OKLA 3K6LA 1ZY0A 5JF7A 3M6RA 1N5NA 1G27A 1VEVA 3G6NA 5JF2A 1S17A 5CXJA 5T8ZA 3PN5A 1Y6HA 4EOXP 5CY7A 5JF5A 4JE6A 5CWYA 2W3TA 3UWBA 1RQCA 5KOBA 3U7MA 1ZY1A 5CVKA 1LM6A 5I2BA 5CP0A 3FWXA 5JEZA 4DR8A 5JF1A 4E9BA 3CPMA 5JF0A 1DFFA 5CPDA 3U04A 3U7NA 4WXLA 3SVJP 1Q1YA 2EW5A 2KMNA 1V3YA 1JYMA 3L87A 4AZ4A 4E9AA 3G5KA 1LMEA 5HGWA 1LQYA 3U7LA 5JEYA 1BS8A 1BSJA 4JE8A 3G5PA 5J46A 5JF8A 1RL4A 3M6OA 1WS0A 2AIAA 1ICJA 1ZXZA 5JF3A 1XEOA 3E3UA 2EW7A 5CY8A 2AI8A 4NT8A 3PN2A 1VEYA 3O3JA 5CX0A 2DEFA 2OS3A 2W3UA 1DEFA 1WS1A 3U7KA 2AIEP 1XENA 4JE7A 1G2AA 5CVQA 5JF6A 3M6PA 1LRYA 5JEXA 4DR9A
chains in the Genus database with same CATH superfamily
5E5DA 1SV2A 1LMHA 4WXKA 1BS5A 3OCAA 1SZZA 3UWAA 3PN6A 3PN3A 2OS0A 3CMDA 1VEZA 2AI7A 4AL2A 1BSZA 2OS1A 5CWXA 2EW6A 4AL3A 5JF4A 1LM4A 3STRP 1LRUA 1BS7A 1BSKA 1BS6A 5CVPA 3PN4A 1XEMA 1LQWA 1BS4A 2AI9A 1IX1A 3QU1A 3M6QA 3SW8P 2OKLA 3K6LA 1ZY0A 5JF7A 3M6RA 1N5NA 1G27A 1VEVA 3G6NA 5JF2A 1S17A 5CXJA 5T8ZA 3PN5A 1Y6HA 4EOXP 5CY7A 5JF5A 4JE6A 5CWYA 2W3TA 3UWBA 1RQCA 5KOBA 3U7MA 1ZY1A 5CVKA 1LM6A 5I2BA 5CP0A 3FWXA 5JEZA 4DR8A 5JF1A 4E9BA 3CPMA 5JF0A 1DFFA 5CPDA 3U04A 3U7NA 4WXLA 3SVJP 1Q1YA 2EW5A 2KMNA 1V3YA 1JYMA 3L87A 4AZ4A 4E9AA 3G5KA 1LMEA 5HGWA 1LQYA 3U7LA 5JEYA 1BS8A 1BSJA 4JE8A 3G5PA 5J46A 5JF8A 1RL4A 3M6OA 1WS0A 2AIAA 1ICJA 1ZXZA 5JF3A 1XEOA 3E3UA 2EW7A 5CY8A 2AI8A 4NT8A 3PN2A 1VEYA 3O3JA 5CX0A 2DEFA 2OS3A 2W3UA 1DEFA 1WS1A 3U7KA 2AIEP 1XENA 4JE7A 1G2AA 5CVQA 5JF6A 3M6PA 1LRYA 5JEXA 4DR9A
chains in the Genus database with same CATH topology
5E5DA 1SV2A 1LMHA 4WXKA 1BS5A 3OCAA 1SZZA 3UWAA 3PN6A 3PN3A 2OS0A 3CMDA 1VEZA 2AI7A 4AL2A 1BSZA 2OS1A 5CWXA 2EW6A 4AL3A 5JF4A 1LM4A 3STRP 1LRUA 1BS7A 1BSKA 1BS6A 5CVPA 3PN4A 1XEMA 1LQWA 1BS4A 2AI9A 1IX1A 3QU1A 3M6QA 3SW8P 2OKLA 3K6LA 1ZY0A 5JF7A 3M6RA 1N5NA 1G27A 1VEVA 3G6NA 5JF2A 1S17A 5CXJA 5T8ZA 3PN5A 1Y6HA 4EOXP 5CY7A 5JF5A 4JE6A 5CWYA 2W3TA 3UWBA 1RQCA 5KOBA 3U7MA 1ZY1A 5CVKA 1LM6A 5I2BA 5CP0A 3FWXA 5JEZA 4DR8A 5JF1A 4E9BA 3CPMA 5JF0A 1DFFA 5CPDA 3U04A 3U7NA 4WXLA 3SVJP 1Q1YA 2EW5A 2KMNA 1V3YA 1JYMA 3L87A 4AZ4A 4E9AA 3G5KA 1LMEA 5HGWA 1LQYA 3U7LA 5JEYA 1BS8A 1BSJA 4JE8A 3G5PA 5J46A 5JF8A 1RL4A 3M6OA 1WS0A 2AIAA 1ICJA 1ZXZA 5JF3A 1XEOA 3E3UA 2EW7A 5CY8A 2AI8A 4NT8A 3PN2A 1VEYA 3O3JA 5CX0A 2DEFA 2OS3A 2W3UA 1DEFA 1WS1A 3U7KA 2AIEP 1XENA 4JE7A 1G2AA 5CVQA 5JF6A 3M6PA 1LRYA 5JEXA 4DR9A
chains in the Genus database with same CATH homology


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