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


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