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


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