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


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