4YNXA

Structure of ydie from e. coli
Total Genus 5
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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
5
sequence length
40
structure length
40
Chain Sequence
PIRRISSQTLLGPDGKLIIDHDGQEYLLRKTQAGKLLLTK
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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 Uncharacterized protein YdiE
publication title The crystal and solution structure of YdiE from Escherichia coli
pubmed doi rcsb
source organism Escherichia coli (strain k12)
molecule tags Unknown function
total genus 5
structure length 40
sequence length 40
chains with identical sequence B
ec nomenclature
pdb deposition date 2015-03-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF10636 hemP Hemin uptake protein hemP
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.10.70.10 Mainly Beta Ribbon Complement Module; domain 1 Complement Module, domain 1 4ynxA00
1ELVA 2G7IA 4LOTA 3SW0X 3L89M 3ZRZA 1HFIA 3OXUD 4AYEA 3M7PA 5HYUB 5HYTB 4AYMA 4C16A 2UWNA 1U5MA 2IZ3A 2LOJA 4AYDA 1Z92B 3T5OA 1C1ZA 2RKYA 2YRAA 1SRZA 2EC3A 2XWJI 2W81A 1TPMA 1PPQA 1OK9A 3CALA 2YBYA 4WJG2 2RL0A 1E5GA 1LY2A 1E88A 1HCCA 1QUBA 2MCZA 3OP8A 1FBRA 2W80A 1OJWA 1OK2A 2XWBF 3NFPI 2WIIC 1GHQB 2QY0A 1E8BA 1UOTP 2RLQA 3ERBA 5HZPB 5FO8C 2KRIA 1HFHA 2MCYA 4ONTD 4PZ5A 4MUCA 4IGDA 3ZD1A 1CKLA 4K12A 1TPGA 3INBC 1MD7A 2CG6A 4CSYA 2B5ID 1H04P 4J38B 2KMSA 4B2RA 1GKGA 2RLPA 3MQLA 1OK1A 4FXGG 1VVCA 3GXEA 1O9AA 2ERJA 2XQWC 1OJVA 3O8EB 2XRBA 2O39C 2CKUA 1ZJKA 2JGWA 1G4FA 5I0QB 1G4GA 3GOVA 4YNXA 2RKZA 4LOSA 1H03P 3IX0A 4JHSA 2CG7A 1SS2A 1QO6A 2JGXA 1QGBA 4DJZA 3IU3I 2BZMA 3KZJA 4A5WB 2XRDA 4B2SA 2EHFA 4F4OC 4KKDA 1OK3A 4AYIA 1GKNA 2IZ4A 1H2QP 3OEDC 3ZD2A 2JRAA 1H2PP 3RJ3D 1Q3XA 3R62A 1NWVA 2V8EA 5HYPA 5JPMG 1MD8A 4ZH1D 1OJYA 1TPNA 3TVJA 1GPZA 1VVDA 2A55A 3KXVA 3EJHA
chains in the Genus database with same CATH superfamily
1ELVA 2G7IA 4LOTA 3SW0X 3ZLEA 3L89M 3ZRZA 1HFIA 4N7EA 4YIZA 3OXUD 4AYEA 3M7PA 5HYUB 5HYTB 4AYMA 4C16A 2UWNA 3ZLDA 1U5MA 2IZ3A 2LOJA 4AYDA 1Z92B 3T5OA 4APLA 1C1ZA 2RKYA 2YRAA 1SRZA 2EC3A 2XWJI 2W81A 1TPMA 1PPQA 1OK9A 3CALA 2YBYA 3FGTA 4WJG2 2RL0A 1E5GA 1LY2A 1E88A 1HCCA 1QUBA 2MCZA 3OP8A 1FBRA 2W80A 1OJWA 1OK2A 2XWBF 3NFPI 3NJAA 2WIIC 1GHQB 4MSLA 2QY0A 2ZYCA 1E8BA 1UOTP 2RLQA 3ERBA 3F6KA 5HZPB 5FO8C 2KRIA 1HFHA 2MCYA 4ONTD 4PZ5A 4MUCA 4IGDA 3ZD1A 1CKLA 4K12A 3K3TA 3CI0J 1TPGA 3INBC 1MD7A 2CG6A 4CSYA 2B5ID 1H04P 4J38B 2KMSA 3WSYA 4B2RA 1GKGA 2RLPA 3MQLA 1OK1A 4FXGG 1VVCA 3GXEA 4PO7A 1O9AA 2ERJA 2Y8TA 2XQWC 2X2ZA 1OJVA 3O8EB 3VWOA 2XRBA 2O39C 2CKUA 1ZJKA 1RLHA 2JGWA 2Y8RA 1G4FA 5I0QB 1G4GA 3GOVA 4YNXA 2RKZA 4LOSA 1H03P 3IX0A 3WSXA 4JHSA 2CG7A 1SS2A 1QO6A 2JGXA 1QGBA 5DN5A 4DJZA 3IU3I 4BWCA 2BZMA 3KZJA 4A5WB 2XRDA 4B2SA 2EHFA 2Y8SA 4F4OC 4KKDA 1OK3A 4AYIA 1GKNA 2IZ4A 1H2QP 3OEDC 3ZD2A 2JRAA 1H2PP 3RJ3D 1Q3XA 3R62A 1NWVA 2V8EA 5HYPA 5JPMG 1MD8A 4ZH1D 1OJYA 1TPNA 3TVJA 1GPZA 1VVDA 2A55A 2I2LA 3FGRA 3KXVA 5DN4A 3EJHA
chains in the Genus database with same CATH topology
1ELVA 2G7IA 4LOTA 3SW0X 3L89M 3ZRZA 1HFIA 3OXUD 4AYEA 3M7PA 5HYUB 5HYTB 4AYMA 4C16A 2UWNA 1U5MA 2IZ3A 2LOJA 4AYDA 1Z92B 3T5OA 1C1ZA 2RKYA 2YRAA 1SRZA 2EC3A 2XWJI 2W81A 1TPMA 1PPQA 1OK9A 3CALA 2YBYA 4WJG2 2RL0A 1E5GA 1LY2A 1E88A 1HCCA 1QUBA 2MCZA 3OP8A 1FBRA 2W80A 1OJWA 1OK2A 2XWBF 3NFPI 2WIIC 1GHQB 2QY0A 1E8BA 1UOTP 2RLQA 3ERBA 5HZPB 5FO8C 2KRIA 1HFHA 2MCYA 4ONTD 4PZ5A 4MUCA 4IGDA 3ZD1A 1CKLA 4K12A 1TPGA 3INBC 1MD7A 2CG6A 4CSYA 2B5ID 1H04P 4J38B 2KMSA 4B2RA 1GKGA 2RLPA 3MQLA 1OK1A 4FXGG 1VVCA 3GXEA 1O9AA 2ERJA 2XQWC 1OJVA 3O8EB 2XRBA 2O39C 2CKUA 1ZJKA 2JGWA 1G4FA 5I0QB 1G4GA 3GOVA 4YNXA 2RKZA 4LOSA 1H03P 3IX0A 4JHSA 2CG7A 1SS2A 1QO6A 2JGXA 1QGBA 4DJZA 3IU3I 2BZMA 3KZJA 4A5WB 2XRDA 4B2SA 2EHFA 4F4OC 4KKDA 1OK3A 4AYIA 1GKNA 2IZ4A 1H2QP 3OEDC 3ZD2A 2JRAA 1H2PP 3RJ3D 1Q3XA 3R62A 1NWVA 2V8EA 5HYPA 5JPMG 1MD8A 4ZH1D 1OJYA 1TPNA 3TVJA 1GPZA 1VVDA 2A55A 3KXVA 3EJHA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1ELV A;  2G7I A;  4LOT A;  3SW0 X;  3L89 M;  3ZRZ A;  1HFI A;  3OXU D;  4AYE A;  3M7P A;  5HYU B;  5HYT B;  4AYM A;  4C16 A;  2UWN A;  1U5M A;  2IZ3 A;  2LOJ A;  4AYD A;  1Z92 B;  3T5O A;  1C1Z A;  2RKY A;  2YRA A;  1SRZ A;  2EC3 A;  2XWJ I;  2W81 A;  1TPM A;  1PPQ A;  1OK9 A;  3CAL A;  2YBY A;  4WJG 2;  2RL0 A;  1E5G A;  1LY2 A;  1E88 A;  1HCC A;  1QUB A;  2MCZ A;  3OP8 A;  1FBR A;  2W80 A;  1OJW A;  1OK2 A;  2XWB F;  3NFP I;  2WII C;  1GHQ B;  2QY0 A;  1E8B A;  1UOT P;  2RLQ A;  3ERB A;  5HZP B;  5FO8 C;  2KRI A;  1HFH A;  2MCY A;  4ONT D;  4PZ5 A;  4MUC A;  4IGD A;  3ZD1 A;  1CKL A;  4K12 A;  1TPG A;  3INB C;  1MD7 A;  2CG6 A;  4CSY A;  2B5I D;  1H04 P;  4J38 B;  2KMS A;  4B2R A;  1GKG A;  2RLP A;  3MQL A;  1OK1 A;  4FXG G;  1VVC A;  3GXE A;  1O9A A;  2ERJ A;  2XQW C;  1OJV A;  3O8E B;  2XRB A;  2O39 C;  2CKU A;  1ZJK A;  2JGW A;  1G4F A;  5I0Q B;  1G4G A;  3GOV A;  4YNX A;  2RKZ A;  4LOS A;  1H03 P;  3IX0 A;  4JHS A;  2CG7 A;  1SS2 A;  1QO6 A;  2JGX A;  1QGB A;  4DJZ A;  3IU3 I;  2BZM A;  3KZJ A;  4A5W B;  2XRD A;  4B2S A;  2EHF A;  4F4O C;  4KKD A;  1OK3 A;  4AYI A;  1GKN A;  2IZ4 A;  1H2Q P;  3OED C;  3ZD2 A;  2JRA A;  1H2P P;  3RJ3 D;  1Q3X A;  3R62 A;  1NWV A;  2V8E A;  5HYP A;  5JPM G;  1MD8 A;  4ZH1 D;  1OJY A;  1TPN A;  3TVJ A;  1GPZ A;  1VVD A;  2A55 A;  3KXV A;  3EJH A; 
#chains in the Genus database with same CATH topology
 1ELV A;  2G7I A;  4LOT A;  3SW0 X;  3ZLE A;  3L89 M;  3ZRZ A;  1HFI A;  4N7E A;  4YIZ A;  3OXU D;  4AYE A;  3M7P A;  5HYU B;  5HYT B;  4AYM A;  4C16 A;  2UWN A;  3ZLD A;  1U5M A;  2IZ3 A;  2LOJ A;  4AYD A;  1Z92 B;  3T5O A;  4APL A;  1C1Z A;  2RKY A;  2YRA A;  1SRZ A;  2EC3 A;  2XWJ I;  2W81 A;  1TPM A;  1PPQ A;  1OK9 A;  3CAL A;  2YBY A;  3FGT A;  4WJG 2;  2RL0 A;  1E5G A;  1LY2 A;  1E88 A;  1HCC A;  1QUB A;  2MCZ A;  3OP8 A;  1FBR A;  2W80 A;  1OJW A;  1OK2 A;  2XWB F;  3NFP I;  3NJA A;  2WII C;  1GHQ B;  4MSL A;  2QY0 A;  2ZYC A;  1E8B A;  1UOT P;  2RLQ A;  3ERB A;  3F6K A;  5HZP B;  5FO8 C;  2KRI A;  1HFH A;  2MCY A;  4ONT D;  4PZ5 A;  4MUC A;  4IGD A;  3ZD1 A;  1CKL A;  4K12 A;  3K3T A;  3CI0 J;  1TPG A;  3INB C;  1MD7 A;  2CG6 A;  4CSY A;  2B5I D;  1H04 P;  4J38 B;  2KMS A;  3WSY A;  4B2R A;  1GKG A;  2RLP A;  3MQL A;  1OK1 A;  4FXG G;  1VVC A;  3GXE A;  4PO7 A;  1O9A A;  2ERJ A;  2Y8T A;  2XQW C;  2X2Z A;  1OJV A;  3O8E B;  3VWO A;  2XRB A;  2O39 C;  2CKU A;  1ZJK A;  1RLH A;  2JGW A;  2Y8R A;  1G4F A;  5I0Q B;  1G4G A;  3GOV A;  4YNX A;  2RKZ A;  4LOS A;  1H03 P;  3IX0 A;  3WSX A;  4JHS A;  2CG7 A;  1SS2 A;  1QO6 A;  2JGX A;  1QGB A;  5DN5 A;  4DJZ A;  3IU3 I;  4BWC A;  2BZM A;  3KZJ A;  4A5W B;  2XRD A;  4B2S A;  2EHF A;  2Y8S A;  4F4O C;  4KKD A;  1OK3 A;  4AYI A;  1GKN A;  2IZ4 A;  1H2Q P;  3OED C;  3ZD2 A;  2JRA A;  1H2P P;  3RJ3 D;  1Q3X A;  3R62 A;  1NWV A;  2V8E A;  5HYP A;  5JPM G;  1MD8 A;  4ZH1 D;  1OJY A;  1TPN A;  3TVJ A;  1GPZ A;  1VVD A;  2A55 A;  2I2L A;  3FGR A;  3KXV A;  5DN4 A;  3EJH A; 
#chains in the Genus database with same CATH homology
 1ELV A;  2G7I A;  4LOT A;  3SW0 X;  3L89 M;  3ZRZ A;  1HFI A;  3OXU D;  4AYE A;  3M7P A;  5HYU B;  5HYT B;  4AYM A;  4C16 A;  2UWN A;  1U5M A;  2IZ3 A;  2LOJ A;  4AYD A;  1Z92 B;  3T5O A;  1C1Z A;  2RKY A;  2YRA A;  1SRZ A;  2EC3 A;  2XWJ I;  2W81 A;  1TPM A;  1PPQ A;  1OK9 A;  3CAL A;  2YBY A;  4WJG 2;  2RL0 A;  1E5G A;  1LY2 A;  1E88 A;  1HCC A;  1QUB A;  2MCZ A;  3OP8 A;  1FBR A;  2W80 A;  1OJW A;  1OK2 A;  2XWB F;  3NFP I;  2WII C;  1GHQ B;  2QY0 A;  1E8B A;  1UOT P;  2RLQ A;  3ERB A;  5HZP B;  5FO8 C;  2KRI A;  1HFH A;  2MCY A;  4ONT D;  4PZ5 A;  4MUC A;  4IGD A;  3ZD1 A;  1CKL A;  4K12 A;  1TPG A;  3INB C;  1MD7 A;  2CG6 A;  4CSY A;  2B5I D;  1H04 P;  4J38 B;  2KMS A;  4B2R A;  1GKG A;  2RLP A;  3MQL A;  1OK1 A;  4FXG G;  1VVC A;  3GXE A;  1O9A A;  2ERJ A;  2XQW C;  1OJV A;  3O8E B;  2XRB A;  2O39 C;  2CKU A;  1ZJK A;  2JGW A;  1G4F A;  5I0Q B;  1G4G A;  3GOV A;  4YNX A;  2RKZ A;  4LOS A;  1H03 P;  3IX0 A;  4JHS A;  2CG7 A;  1SS2 A;  1QO6 A;  2JGX A;  1QGB A;  4DJZ A;  3IU3 I;  2BZM A;  3KZJ A;  4A5W B;  2XRD A;  4B2S A;  2EHF A;  4F4O C;  4KKD A;  1OK3 A;  4AYI A;  1GKN A;  2IZ4 A;  1H2Q P;  3OED C;  3ZD2 A;  2JRA A;  1H2P P;  3RJ3 D;  1Q3X A;  3R62 A;  1NWV A;  2V8E A;  5HYP A;  5JPM G;  1MD8 A;  4ZH1 D;  1OJY A;  1TPN A;  3TVJ A;  1GPZ A;  1VVD A;  2A55 A;  3KXV A;  3EJH 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)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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