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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molecule tags Hydrolase
molecule keywords O-acetyl-ADP-ribose deacetylase
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
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
3EWQA 3V2BA 4GVVA 2J9AA 5D8NA 2EEEA 5E3BA 4K3NA 4X2TA 3H8FA 2ACFA 2DX6A 5CB3A 3SIIA 5HOLA 3GQEA 3PEIA 3KZWA 4ZI6A 3IIFA 1TY8A 4ZX9A 2BFQA 4GUAA 3H8EA 3H8GA 4R76A 3T8WA 1LCPA 3GPGA 1LAMA 3SIGA 2FG1A 1ZR5A 1SPVA 1LANA 1ZR3A 3JZTA 4KYBA 3KQZA 5AILA 1GYTA 2BFRA 2AFCA 2EWBA 1LAPA 5DUSA 4ZYQA 5CBMA 4J5QA 2XD7A 3GPQA 4D86A 4ABLA 3KQXA 1TXZA 3EWPA 4ESSA 4JLLA 3SIJA 3EWRA 4J5SA 3EKEA 1HJZA 3Q71A 4ETJA 4J5RA 3JRUA 3GQOA 4IQYA 4R6TA 1YD9A 3IIDA 4UMLA 4JVVA 4R7MA 3KR5A 5HIHA 1VHUA 3EWOA 5FSZA 4ZY2A 3EW5A 3Q6ZA 4ETKA 4TU0A 5FSVA 4ZX8A 4JGKA 4GVWA 5FSUA 3ETIA 5FSXA 3V45A 3EJGA 5CB5A 1BPMA 3IJ3A 2LGRA 4ABKA 5CMSA 3EJFA 4K0CA 4J4ZA 1BPNA 5FSYA 2VRIA 2FAVA 4JCAA 3VFQA 2FXKA 1NJRA 2L8RA 3KR4A 4ZY0A 3SIHA 4KSIA 1BLLE 2X47A 3GPOA 4ZY1A
chains in the Genus database with same CATH superfamily
3EWQA 3V2BA 4GVVA 2J9AA 5D8NA 2EEEA 5E3BA 4K3NA 4X2TA 3H8FA 2ACFA 2DX6A 5CB3A 3SIIA 5HOLA 3GQEA 3PEIA 3KZWA 4ZI6A 3IIFA 1TY8A 4ZX9A 2BFQA 4GUAA 3H8EA 3H8GA 2WCTA 4R76A 2RNKA 3T8WA 1LCPA 3GPGA 1LAMA 3SIGA 2FG1A 1ZR5A 2JZFA 1SPVA 1LANA 1ZR3A 3JZTA 4KYBA 3KQZA 5AILA 1GYTA 2BFRA 2AFCA 2EWBA 1LAPA 2W2GA 5DUSA 4ZYQA 5CBMA 4J5QA 2XD7A 3GPQA 4D86A 4ABLA 3KQXA 1TXZA 3EWPA 4ESSA 4JLLA 3SIJA 3EWRA 4J5SA 3EKEA 1HJZA 3Q71A 4ETJA 4J5RA 3JRUA 3GQOA 4IQYA 4R6TA 1YD9A 3IIDA 4UMLA 4JVVA 4R7MA 3KR5A 5HIHA 1VHUA 3EWOA 5FSZA 4ZY2A 3EW5A 3Q6ZA 4ETKA 4TU0A 5FSVA 4ZX8A 4JGKA 4GVWA 5FSUA 3ETIA 5FSXA 3V45A 3EJGA 5CB5A 1BPMA 3IJ3A 2LGRA 4ABKA 5CMSA 3EJFA 4K0CA 4J4ZA 1BPNA 5FSYA 2VRIA 2FAVA 4JCAA 2JZDA 3VFQA 2FXKA 2JZEA 1NJRA 2L8RA 3KR4A 4ZY0A 3SIHA 2KQVA 4KSIA 1BLLE 2X47A 3GPOA 4ZY1A
chains in the Genus database with same CATH topology
3EWQA 3V2BA 4GVVA 2J9AA 5D8NA 2EEEA 5E3BA 4K3NA 4X2TA 3H8FA 2ACFA 2DX6A 5CB3A 3SIIA 5HOLA 3GQEA 3PEIA 3KZWA 4ZI6A 3IIFA 1TY8A 4ZX9A 2BFQA 4GUAA 3H8EA 3H8GA 4R76A 3T8WA 1LCPA 3GPGA 1LAMA 3SIGA 2FG1A 1ZR5A 1SPVA 1LANA 1ZR3A 3JZTA 4KYBA 3KQZA 5AILA 1GYTA 2BFRA 2AFCA 2EWBA 1LAPA 5DUSA 4ZYQA 5CBMA 4J5QA 2XD7A 3GPQA 4D86A 4ABLA 3KQXA 1TXZA 3EWPA 4ESSA 4JLLA 3SIJA 3EWRA 4J5SA 3EKEA 1HJZA 3Q71A 4ETJA 4J5RA 3JRUA 3GQOA 4IQYA 4R6TA 1YD9A 3IIDA 4UMLA 4JVVA 4R7MA 3KR5A 5HIHA 1VHUA 3EWOA 5FSZA 4ZY2A 3EW5A 3Q6ZA 4ETKA 4TU0A 5FSVA 4ZX8A 4JGKA 4GVWA 5FSUA 3ETIA 5FSXA 3V45A 3EJGA 5CB5A 1BPMA 3IJ3A 2LGRA 4ABKA 5CMSA 3EJFA 4K0CA 4J4ZA 1BPNA 5FSYA 2VRIA 2FAVA 4JCAA 3VFQA 2FXKA 1NJRA 2L8RA 3KR4A 4ZY0A 3SIHA 4KSIA 1BLLE 2X47A 3GPOA 4ZY1A
chains in the Genus database with same CATH homology


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