5CB5A

Structural insights into the mechanism of escherichia coli ymdb
Total Genus 52
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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
52
sequence length
173
structure length
173
Chain Sequence
KTRIHVVQGDITKLAVDVIVNAAAPSLMGGGGVAGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQQ
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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 52
structure length 173
sequence length 173
chains with identical sequence B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
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 5cb5A00
5HIHA 5FSZA 4J5SA 4K0CA 1LAPA 2ACFA 3H8GA 3SIGA 1YD9A 3KZWA 2FG1A 3GQEA 3SIHA 2BFQA 4ZY2A 4JGKA 3ETIA 5CBMA 1BPMA 4KSIA 3EWQA 3EWOA 3JRUA 1SPVA 3IJ3A 4R6TA 3KQXA 5CB3A 4GVWA 4ETJA 4UMLA 3GPOA 4ZI6A 1GYTA 3EJFA 4ABLA 3KR5A 4ZY0A 3JZTA 3GQOA 2L8RA 4KYBA 3IIFA 3H8FA 2BFRA 3EWPA 3Q71A 3V45A 4X2TA 3KR4A 4J4ZA 3PEIA 4JLLA 2AFCA 4JVVA 1BPNA 5FSXA 4TU0A 4ESSA 3V2BA 3SIJA 3SIIA 2EWBA 1LCPA 1NJRA 2LGRA 3GPQA 3KQZA 5CMSA 3GPGA 1ZR3A 3H8EA 3VFQA 1LANA 2DX6A 3EJGA 4R76A 5HOLA 1TY8A 2VRIA 5FSUA 3EWRA 4R7MA 1LAMA 4J5RA 4ZYQA 4ZY1A 5CB5A 4GVVA 3T8WA 4ZX9A 5D8NA 1HJZA 4J5QA 3EKEA 5AILA 1TXZA 1BLLE 4JCAA 4D86A 2X47A 5E3BA 3EW5A 3IIDA 1VHUA 4IQYA 4ETKA 3Q6ZA 4ZX8A 2XD7A 5FSYA 4ABKA 5FSVA 4K3NA 2J9AA 2EEEA 4GUAA 2FAVA 1ZR5A 2FXKA 5DUSA
chains in the Genus database with same CATH superfamily
5HIHA 5FSZA 4J5SA 4K0CA 1LAPA 2JZDA 2ACFA 3H8GA 3SIGA 1YD9A 3KZWA 2FG1A 3GQEA 3SIHA 2BFQA 4ZY2A 4JGKA 2RNKA 3ETIA 5CBMA 1BPMA 4KSIA 3EWQA 3EWOA 3JRUA 2JZEA 1SPVA 3IJ3A 4R6TA 3KQXA 5CB3A 4GVWA 4ETJA 4UMLA 3GPOA 4ZI6A 1GYTA 3EJFA 4ABLA 3KR5A 4ZY0A 3JZTA 3GQOA 2L8RA 4KYBA 3IIFA 3H8FA 2BFRA 3EWPA 3Q71A 3V45A 4X2TA 3KR4A 4J4ZA 2KQVA 3PEIA 4JLLA 2AFCA 4JVVA 1BPNA 5FSXA 4TU0A 2JZFA 4ESSA 3V2BA 3SIJA 3SIIA 2EWBA 1LCPA 1NJRA 2LGRA 3GPQA 3KQZA 5CMSA 3GPGA 1ZR3A 3H8EA 3VFQA 1LANA 2DX6A 3EJGA 4R76A 5HOLA 1TY8A 2VRIA 5FSUA 3EWRA 2WCTA 4R7MA 1LAMA 4J5RA 4ZYQA 4ZY1A 5CB5A 4GVVA 3T8WA 4ZX9A 5D8NA 2W2GA 1HJZA 4J5QA 3EKEA 5AILA 1TXZA 1BLLE 4JCAA 4D86A 2X47A 5E3BA 3EW5A 3IIDA 1VHUA 4IQYA 4ETKA 3Q6ZA 4ZX8A 2XD7A 5FSYA 4ABKA 5FSVA 4K3NA 2J9AA 2EEEA 4GUAA 2FAVA 1ZR5A 2FXKA 5DUSA
chains in the Genus database with same CATH topology
5HIHA 5FSZA 4J5SA 4K0CA 1LAPA 2ACFA 3H8GA 3SIGA 1YD9A 3KZWA 2FG1A 3GQEA 3SIHA 2BFQA 4ZY2A 4JGKA 3ETIA 5CBMA 1BPMA 4KSIA 3EWQA 3EWOA 3JRUA 1SPVA 3IJ3A 4R6TA 3KQXA 5CB3A 4GVWA 4ETJA 4UMLA 3GPOA 4ZI6A 1GYTA 3EJFA 4ABLA 3KR5A 4ZY0A 3JZTA 3GQOA 2L8RA 4KYBA 3IIFA 3H8FA 2BFRA 3EWPA 3Q71A 3V45A 4X2TA 3KR4A 4J4ZA 3PEIA 4JLLA 2AFCA 4JVVA 1BPNA 5FSXA 4TU0A 4ESSA 3V2BA 3SIJA 3SIIA 2EWBA 1LCPA 1NJRA 2LGRA 3GPQA 3KQZA 5CMSA 3GPGA 1ZR3A 3H8EA 3VFQA 1LANA 2DX6A 3EJGA 4R76A 5HOLA 1TY8A 2VRIA 5FSUA 3EWRA 4R7MA 1LAMA 4J5RA 4ZYQA 4ZY1A 5CB5A 4GVVA 3T8WA 4ZX9A 5D8NA 1HJZA 4J5QA 3EKEA 5AILA 1TXZA 1BLLE 4JCAA 4D86A 2X47A 5E3BA 3EW5A 3IIDA 1VHUA 4IQYA 4ETKA 3Q6ZA 4ZX8A 2XD7A 5FSYA 4ABKA 5FSVA 4K3NA 2J9AA 2EEEA 4GUAA 2FAVA 1ZR5A 2FXKA 5DUSA
chains in the Genus database with same CATH homology


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