5CB3A

Structural insights into the mechanism of escherichia coli ymdb
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
171
structure length
171
Chain Sequence
TRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQ
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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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publication title Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
pubmed doi rcsb
source organism Escherichia coli k12
molecule tags Hydrolase
molecule keywords O-acetyl-ADP-ribose deacetylase
total genus 56
structure length 171
sequence length 171
ec nomenclature ec 3.5.1.-:
pdb deposition date 2015-06-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01661 Macro Macro domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.220.10 Alpha Beta 3-Layer(aba) Sandwich Leucine Aminopeptidase, subunit E; domain 1 Leucine Aminopeptidase, subunit E, domain 1 5cb3A00
3KR4A 4K0CA 3VFQA 4ESSA 1TXZA 2L8RA 2FG1A 4GUAA 4KYBA 1ZR3A 4J4ZA 4ZI6A 4K3NA 4ABLA 3ETIA 3GPQA 4JLLA 3SIHA 2BFQA 1LAPA 3KR5A 1TY8A 3IIFA 5HOLA 2VRIA 3EWOA 5FSVA 2ACFA 3T8WA 2X47A 4ABKA 5FSXA 1VHUA 5CB3A 3H8EA 4J5SA 1SPVA 1LCPA 5DUSA 5AILA 4ZY1A 3IJ3A 3JZTA 2EEEA 4ZY2A 3H8FA 1BPNA 1YD9A 3GQOA 1BPMA 4D86A 1LAMA 3Q6ZA 3SIGA 4ETKA 3EW5A 3H8GA 3V2BA 4JCAA 3EWPA 5FSYA 2DX6A 1NJRA 3EKEA 4TU0A 2BFRA 5HIHA 4J5QA 3GQEA 4ZX8A 5FSUA 3JRUA 4ETJA 4KSIA 4GVVA 1GYTA 4R76A 1LANA 4X2TA 4UMLA 3KQZA 4R6TA 3PEIA 5CBMA 4GVWA 3EWQA 2J9AA 4J5RA 4JVVA 2FAVA 3SIJA 3GPOA 4JGKA 1ZR5A 2AFCA 2FXKA 5D8NA 3GPGA 3IIDA 3KQXA 3Q71A 3V45A 3EJGA 1BLLE 4ZY0A 4ZX9A 4ZYQA 5FSZA 5CB5A 4IQYA 3KZWA 3EWRA 1HJZA 3SIIA 2LGRA 5CMSA 4R7MA 5E3BA 2EWBA 2XD7A 3EJFA
chains in the Genus database with same CATH superfamily
3KR4A 4K0CA 3VFQA 4ESSA 1TXZA 2KQVA 2L8RA 2FG1A 4GUAA 4KYBA 1ZR3A 4J4ZA 4ZI6A 4K3NA 4ABLA 3ETIA 3GPQA 4JLLA 3SIHA 2BFQA 1LAPA 3KR5A 1TY8A 3IIFA 5HOLA 2VRIA 3EWOA 5FSVA 2ACFA 3T8WA 2X47A 4ABKA 5FSXA 2WCTA 1VHUA 5CB3A 3H8EA 4J5SA 1SPVA 1LCPA 5DUSA 5AILA 4ZY1A 3IJ3A 3JZTA 2EEEA 4ZY2A 3H8FA 1BPNA 1YD9A 3GQOA 1BPMA 4D86A 1LAMA 3Q6ZA 3SIGA 4ETKA 3EW5A 3H8GA 3V2BA 4JCAA 3EWPA 5FSYA 2JZEA 2DX6A 1NJRA 3EKEA 4TU0A 2RNKA 2BFRA 5HIHA 4J5QA 3GQEA 4ZX8A 5FSUA 3JRUA 4ETJA 4KSIA 4GVVA 1GYTA 4R76A 1LANA 4X2TA 4UMLA 3KQZA 3PEIA 4R6TA 5CBMA 4GVWA 3EWQA 2J9AA 4J5RA 4JVVA 2JZDA 2FAVA 3SIJA 3GPOA 4JGKA 1ZR5A 2AFCA 2FXKA 5D8NA 3GPGA 3IIDA 3KQXA 3Q71A 3V45A 2JZFA 1BLLE 3EJGA 4ZY0A 4ZX9A 4ZYQA 5FSZA 5CB5A 4IQYA 3KZWA 3EWRA 1HJZA 3SIIA 2LGRA 2W2GA 5CMSA 4R7MA 5E3BA 2EWBA 2XD7A 3EJFA
chains in the Genus database with same CATH topology
3KR4A 4K0CA 3VFQA 4ESSA 1TXZA 2L8RA 2FG1A 4GUAA 4KYBA 1ZR3A 4J4ZA 4ZI6A 4K3NA 4ABLA 3ETIA 3GPQA 4JLLA 3SIHA 2BFQA 1LAPA 3KR5A 1TY8A 3IIFA 5HOLA 2VRIA 3EWOA 5FSVA 2ACFA 3T8WA 2X47A 4ABKA 5FSXA 1VHUA 5CB3A 3H8EA 4J5SA 1SPVA 1LCPA 5DUSA 5AILA 4ZY1A 3IJ3A 3JZTA 2EEEA 4ZY2A 3H8FA 1BPNA 1YD9A 3GQOA 1BPMA 4D86A 1LAMA 3Q6ZA 3SIGA 4ETKA 3EW5A 3H8GA 3V2BA 4JCAA 3EWPA 5FSYA 2DX6A 1NJRA 3EKEA 4TU0A 2BFRA 5HIHA 4J5QA 3GQEA 4ZX8A 5FSUA 3JRUA 4ETJA 4KSIA 4GVVA 1GYTA 4R76A 1LANA 4X2TA 4UMLA 3KQZA 4R6TA 3PEIA 5CBMA 4GVWA 3EWQA 2J9AA 4J5RA 4JVVA 2FAVA 3SIJA 3GPOA 4JGKA 1ZR5A 2AFCA 2FXKA 5D8NA 3GPGA 3IIDA 3KQXA 3Q71A 3V45A 3EJGA 1BLLE 4ZY0A 4ZX9A 4ZYQA 5FSZA 5CB5A 4IQYA 3KZWA 3EWRA 1HJZA 3SIIA 2LGRA 5CMSA 4R7MA 5E3BA 2EWBA 2XD7A 3EJFA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3KR4 A;  4K0C A;  3VFQ A;  4ESS A;  1TXZ A;  2L8R A;  2FG1 A;  4GUA A;  4KYB A;  1ZR3 A;  4J4Z A;  4ZI6 A;  4K3N A;  4ABL A;  3ETI A;  3GPQ A;  4JLL A;  3SIH A;  2BFQ A;  1LAP A;  3KR5 A;  1TY8 A;  3IIF A;  5HOL A;  2VRI A;  3EWO A;  5FSV A;  2ACF A;  3T8W A;  2X47 A;  4ABK A;  5FSX A;  1VHU A;  5CB3 A;  3H8E A;  4J5S A;  1SPV A;  1LCP A;  5DUS A;  5AIL A;  4ZY1 A;  3IJ3 A;  3JZT A;  2EEE A;  4ZY2 A;  3H8F A;  1BPN A;  1YD9 A;  3GQO A;  1BPM A;  4D86 A;  1LAM A;  3Q6Z A;  3SIG A;  4ETK A;  3EW5 A;  3H8G A;  3V2B A;  4JCA A;  3EWP A;  5FSY A;  2DX6 A;  1NJR A;  3EKE A;  4TU0 A;  2BFR A;  5HIH A;  4J5Q A;  3GQE A;  4ZX8 A;  5FSU A;  3JRU A;  4ETJ A;  4KSI A;  4GVV A;  1GYT A;  4R76 A;  1LAN A;  4X2T A;  4UML A;  3KQZ A;  4R6T A;  3PEI A;  5CBM A;  4GVW A;  3EWQ A;  2J9A A;  4J5R A;  4JVV A;  2FAV A;  3SIJ A;  3GPO A;  4JGK A;  1ZR5 A;  2AFC A;  2FXK A;  5D8N A;  3GPG A;  3IID A;  3KQX A;  3Q71 A;  3V45 A;  3EJG A;  1BLL E;  4ZY0 A;  4ZX9 A;  4ZYQ A;  5FSZ A;  5CB5 A;  4IQY A;  3KZW A;  3EWR A;  1HJZ A;  3SII A;  2LGR A;  5CMS A;  4R7M A;  5E3B A;  2EWB A;  2XD7 A;  3EJF A; 
#chains in the Genus database with same CATH topology
 3KR4 A;  4K0C A;  3VFQ A;  4ESS A;  1TXZ A;  2KQV A;  2L8R A;  2FG1 A;  4GUA A;  4KYB A;  1ZR3 A;  4J4Z A;  4ZI6 A;  4K3N A;  4ABL A;  3ETI A;  3GPQ A;  4JLL A;  3SIH A;  2BFQ A;  1LAP A;  3KR5 A;  1TY8 A;  3IIF A;  5HOL A;  2VRI A;  3EWO A;  5FSV A;  2ACF A;  3T8W A;  2X47 A;  4ABK A;  5FSX A;  2WCT A;  1VHU A;  5CB3 A;  3H8E A;  4J5S A;  1SPV A;  1LCP A;  5DUS A;  5AIL A;  4ZY1 A;  3IJ3 A;  3JZT A;  2EEE A;  4ZY2 A;  3H8F A;  1BPN A;  1YD9 A;  3GQO A;  1BPM A;  4D86 A;  1LAM A;  3Q6Z A;  3SIG A;  4ETK A;  3EW5 A;  3H8G A;  3V2B A;  4JCA A;  3EWP A;  5FSY A;  2JZE A;  2DX6 A;  1NJR A;  3EKE A;  4TU0 A;  2RNK A;  2BFR A;  5HIH A;  4J5Q A;  3GQE A;  4ZX8 A;  5FSU A;  3JRU A;  4ETJ A;  4KSI A;  4GVV A;  1GYT A;  4R76 A;  1LAN A;  4X2T A;  4UML A;  3KQZ A;  3PEI A;  4R6T A;  5CBM A;  4GVW A;  3EWQ A;  2J9A A;  4J5R A;  4JVV A;  2JZD A;  2FAV A;  3SIJ A;  3GPO A;  4JGK A;  1ZR5 A;  2AFC A;  2FXK A;  5D8N A;  3GPG A;  3IID A;  3KQX A;  3Q71 A;  3V45 A;  2JZF A;  1BLL E;  3EJG A;  4ZY0 A;  4ZX9 A;  4ZYQ A;  5FSZ A;  5CB5 A;  4IQY A;  3KZW A;  3EWR A;  1HJZ A;  3SII A;  2LGR A;  2W2G A;  5CMS A;  4R7M A;  5E3B A;  2EWB A;  2XD7 A;  3EJF A; 
#chains in the Genus database with same CATH homology
 3KR4 A;  4K0C A;  3VFQ A;  4ESS A;  1TXZ A;  2L8R A;  2FG1 A;  4GUA A;  4KYB A;  1ZR3 A;  4J4Z A;  4ZI6 A;  4K3N A;  4ABL A;  3ETI A;  3GPQ A;  4JLL A;  3SIH A;  2BFQ A;  1LAP A;  3KR5 A;  1TY8 A;  3IIF A;  5HOL A;  2VRI A;  3EWO A;  5FSV A;  2ACF A;  3T8W A;  2X47 A;  4ABK A;  5FSX A;  1VHU A;  5CB3 A;  3H8E A;  4J5S A;  1SPV A;  1LCP A;  5DUS A;  5AIL A;  4ZY1 A;  3IJ3 A;  3JZT A;  2EEE A;  4ZY2 A;  3H8F A;  1BPN A;  1YD9 A;  3GQO A;  1BPM A;  4D86 A;  1LAM A;  3Q6Z A;  3SIG A;  4ETK A;  3EW5 A;  3H8G A;  3V2B A;  4JCA A;  3EWP A;  5FSY A;  2DX6 A;  1NJR A;  3EKE A;  4TU0 A;  2BFR A;  5HIH A;  4J5Q A;  3GQE A;  4ZX8 A;  5FSU A;  3JRU A;  4ETJ A;  4KSI A;  4GVV A;  1GYT A;  4R76 A;  1LAN A;  4X2T A;  4UML A;  3KQZ A;  4R6T A;  3PEI A;  5CBM A;  4GVW A;  3EWQ A;  2J9A A;  4J5R A;  4JVV A;  2FAV A;  3SIJ A;  3GPO A;  4JGK A;  1ZR5 A;  2AFC A;  2FXK A;  5D8N A;  3GPG A;  3IID A;  3KQX A;  3Q71 A;  3V45 A;  3EJG A;  1BLL E;  4ZY0 A;  4ZX9 A;  4ZYQ A;  5FSZ A;  5CB5 A;  4IQY A;  3KZW A;  3EWR A;  1HJZ A;  3SII A;  2LGR A;  5CMS A;  4R7M A;  5E3B A;  2EWB A;  2XD7 A;  3EJF A; 
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similar chains in the Genus database (?% sequence similarity)
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