5CMSA

Structural insights into the mechanism of escherichia coli ymdb
Total Genus 53
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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
53
sequence length
173
structure length
173
Chain Sequence
b'KTRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVAGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQQ'
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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
molecule tags Hydrolase
source organism Escherichia coli
publication title Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase
pubmed doi rcsb
total genus 53
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 2015-07-17

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 5cmsA00
1HJZA 1TXZA 2DX6A 4R7MA 3SIGA 3H8GA 5D8NA 4ZX8A 4ZY0A 3H8FA 4ZYQA 3EWRA 3IIFA 4ETJA 3SIIA 2AFCA 4GUAA 4IQYA 1GYTA 5CB3A 1LAPA 4ZX9A 4X2TA 4ABLA 3SIHA 5AILA 4J5QA 3V2BA 3KR5A 1BPNA 4R6TA 5HOLA 3EKEA 3EWPA 3KR4A 4ABKA 5HIHA 4ZY2A 3KZWA 4J4ZA 2X47A 4GVVA 3IJ3A 1LANA 1LAMA 2LGRA 4TU0A 3GPQA 4GVWA 2EEEA 2ACFA 2FAVA 3JRUA 2FG1A 4JGKA 3GQOA 3ETIA 1NJRA 3GPGA 2BFQA 2FXKA 5FSYA 4K3NA 1BLLE 4KSIA 5FSUA 4JLLA 4J5RA 3VFQA 1TY8A 1SPVA 3EJFA 3Q6ZA 3Q71A 4ETKA 4K0CA 5CMSA 4KYBA 3T8WA 4ESSA 5CBMA 2L8RA 1ZR5A 3PEIA 2EWBA 1BPMA 5E3BA 1LCPA 3EWQA 4ZI6A 3EW5A 5FSXA 2J9AA 3EJGA 4R76A 3H8EA 4J5SA 5CB5A 4UMLA 4JCAA 3KQZA 2VRIA 3JZTA 3IIDA 3V45A 1ZR3A 1VHUA 3EWOA 5FSZA 4JVVA 5DUSA 3GPOA 2XD7A 5FSVA 3SIJA 1YD9A 4D86A 2BFRA 4ZY1A 3GQEA 3KQXA
chains in the Genus database with same CATH superfamily
1HJZA 1TXZA 2DX6A 2JZDA 4R7MA 3SIGA 3H8GA 5D8NA 4ZX8A 4ZY0A 3H8FA 4ZYQA 3EWRA 3IIFA 4ETJA 3SIIA 2AFCA 4GUAA 4IQYA 1GYTA 5CB3A 1LAPA 4ZX9A 4X2TA 4ABLA 3SIHA 5AILA 4J5QA 3V2BA 3KR5A 1BPNA 4R6TA 5HOLA 3EKEA 2WCTA 3EWPA 3KR4A 4ABKA 5HIHA 4ZY2A 3KZWA 4J4ZA 2X47A 4GVVA 3IJ3A 1LANA 1LAMA 2LGRA 4TU0A 3GPQA 4GVWA 2EEEA 2ACFA 2FAVA 3JRUA 2FG1A 4JGKA 3GQOA 3ETIA 1NJRA 3GPGA 2JZFA 2BFQA 2FXKA 5FSYA 4K3NA 1BLLE 4KSIA 5FSUA 2KQVA 4JLLA 4J5RA 3VFQA 1TY8A 1SPVA 3EJFA 3Q6ZA 3Q71A 4ETKA 4K0CA 5CMSA 4KYBA 3T8WA 4ESSA 5CBMA 2L8RA 1ZR5A 3PEIA 2EWBA 1BPMA 5E3BA 1LCPA 3EWQA 4ZI6A 3EW5A 5FSXA 2J9AA 3EJGA 4R76A 3H8EA 4J5SA 5CB5A 4UMLA 4JCAA 3KQZA 2JZEA 2VRIA 3JZTA 3IIDA 2RNKA 3V45A 1ZR3A 1VHUA 3EWOA 2W2GA 5FSZA 4JVVA 5DUSA 3GPOA 2XD7A 5FSVA 3SIJA 1YD9A 4D86A 2BFRA 4ZY1A 3GQEA 3KQXA
chains in the Genus database with same CATH topology
1HJZA 1TXZA 2DX6A 4R7MA 3SIGA 3H8GA 5D8NA 4ZX8A 4ZY0A 3H8FA 4ZYQA 3EWRA 3IIFA 4ETJA 3SIIA 2AFCA 4GUAA 4IQYA 1GYTA 5CB3A 1LAPA 4ZX9A 4X2TA 4ABLA 3SIHA 5AILA 4J5QA 3V2BA 3KR5A 1BPNA 4R6TA 5HOLA 3EKEA 3EWPA 3KR4A 4ABKA 5HIHA 4ZY2A 3KZWA 4J4ZA 2X47A 4GVVA 3IJ3A 1LANA 1LAMA 2LGRA 4TU0A 3GPQA 4GVWA 2EEEA 2ACFA 2FAVA 3JRUA 2FG1A 4JGKA 3GQOA 3ETIA 1NJRA 3GPGA 2BFQA 2FXKA 5FSYA 4K3NA 1BLLE 4KSIA 5FSUA 4JLLA 4J5RA 3VFQA 1TY8A 1SPVA 3EJFA 3Q6ZA 3Q71A 4ETKA 4K0CA 5CMSA 4KYBA 3T8WA 4ESSA 5CBMA 2L8RA 1ZR5A 3PEIA 2EWBA 1BPMA 5E3BA 1LCPA 3EWQA 4ZI6A 3EW5A 5FSXA 2J9AA 3EJGA 4R76A 3H8EA 4J5SA 5CB5A 4UMLA 4JCAA 3KQZA 2VRIA 3JZTA 3IIDA 3V45A 1ZR3A 1VHUA 3EWOA 5FSZA 4JVVA 5DUSA 3GPOA 2XD7A 5FSVA 3SIJA 1YD9A 4D86A 2BFRA 4ZY1A 3GQEA 3KQXA
chains in the Genus database with same CATH homology


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