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


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