1QY9A

Crystal structure of e. coli se-met protein ydde
Total Genus 77
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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
77
sequence length
295
structure length
295
Chain Sequence
PQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL
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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 Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase
pubmed doi rcsb
source organism Escherichia coli
molecule tags Unknown function
molecule keywords HYPOTHETICAL PROTEIN yddE
total genus 77
structure length 295
sequence length 295
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2003-09-10

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02567 PhzC-PhzF Phenazine biosynthesis-like protein
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 1qy9A01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 1qy9A02
1S7JA 1U1VA 2Q9JA 2GKEA 4JBDA 4JCIA 3EKMA 1U0KA 2PW0A 4IK0A 4Q60A 4J9WA 1YM5A 2H9FA 5M47A 3EJXA 1GQZA 1QYAA 1XUAA 4JUUA 1SDJA 1T6KA 2PVZA 3G7KA 4IJZA 4J9XA 4K7XA 5HA4A 5H2GA 1TM0A 1W62A 4DUNA 1U1WA 3FVEA 1U1XA 1W61A 5IWEA 3EDNA 1BWZA 2AZPA 1XUBA 2GKJA 4K8LA 2OTNA 4Q2HA 4LB0A 4K7GB 5H2YA 4JD7A 2Q9HA 1QY9A
chains in the Genus database with same CATH superfamily
1S7JA 2KW7A 3EKMA 2ZVFA 2ZXPA 2QB7A 4JUUA 3ICJA 3WQZA 4DUNA 3W5WA 2ENXA 1U1XA 1WPMA 2MPBA 3IGHX 5IWEA 4K8LA 4GL6A 1I74A 3PTJA 1U1VA 2Q9JA 4JCIA 2PW0A 4Q60A 1YM5A 2H9FA 3EJXA 1XUAA 1IR6A 5HA4A 1SDJA 4K7XA 1U1WA 1K23A 2ZXOA 1K20A 2AZPA 1XUBA 2GKJA 4LB0A 4JD7A 2HAWA 2GKEA 4JBDA 4PY9A 2QB6A 1U0KA 4LG3A 2IW4A 2KPTA 3G98A 1GQZA 2QB8A 1QYAA 5H2GA 3G7KA 4IJZA 2LT2A 4OA3A 1TM0A 4RPAA 1WPPA 1BWZA 5ANPA 4LS9A 4K7GB 2Q9HA 1QY9A 4IK0A 4J9WA 5M47A 3PVHA 3DEVA 2ZXRA 1T6KA 2EB0A 2PVZA 4J9XA 1W62A 3FVEA 1W61A 3EDNA 2YMAA 2OTNA 4Q2HA 3PW9A 5H2YA
chains in the Genus database with same CATH topology
1S7JA 2KW7A 3EKMA 2ZVFA 2ZXPA 2QB7A 4JUUA 3ICJA 3WQZA 4DUNA 3W5WA 2ENXA 1U1XA 1WPMA 2MPBA 3IGHX 5IWEA 4K8LA 4GL6A 1I74A 3PTJA 1U1VA 2Q9JA 4JCIA 2PW0A 4Q60A 1YM5A 2H9FA 3EJXA 1XUAA 1IR6A 5HA4A 1SDJA 4K7XA 1U1WA 1K23A 2ZXOA 1K20A 2AZPA 1XUBA 2GKJA 4LB0A 4JD7A 2HAWA 2GKEA 4JBDA 4PY9A 2QB6A 1U0KA 4LG3A 2IW4A 2KPTA 3G98A 1GQZA 2QB8A 1QYAA 5H2GA 3G7KA 4IJZA 2LT2A 4OA3A 1TM0A 4RPAA 1WPPA 1BWZA 5ANPA 4LS9A 4K7GB 2Q9HA 1QY9A 4IK0A 4J9WA 5M47A 3PVHA 3DEVA 2ZXRA 1T6KA 2EB0A 2PVZA 4J9XA 1W62A 3FVEA 1W61A 3EDNA 2YMAA 2OTNA 4Q2HA 3PW9A 5H2YA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1S7J A;  1U1V A;  2Q9J A;  2GKE A;  4JBD A;  4JCI A;  3EKM A;  1U0K A;  2PW0 A;  4IK0 A;  4Q60 A;  4J9W A;  1YM5 A;  2H9F A;  5M47 A;  3EJX A;  1GQZ A;  1QYA A;  1XUA A;  4JUU A;  1SDJ A;  1T6K A;  2PVZ A;  3G7K A;  4IJZ A;  4J9X A;  4K7X A;  5HA4 A;  5H2G A;  1TM0 A;  1W62 A;  4DUN A;  1U1W A;  3FVE A;  1U1X A;  1W61 A;  5IWE A;  3EDN A;  1BWZ A;  2AZP A;  1XUB A;  2GKJ A;  4K8L A;  2OTN A;  4Q2H A;  4LB0 A;  4K7G B;  5H2Y A;  4JD7 A;  2Q9H A;  1QY9 A; 
#chains in the Genus database with same CATH topology
 1S7J A;  2KW7 A;  3EKM A;  2ZVF A;  2ZXP A;  2QB7 A;  4JUU A;  3ICJ A;  3WQZ A;  4DUN A;  3W5W A;  2ENX A;  1U1X A;  1WPM A;  2MPB A;  3IGH X;  5IWE A;  4K8L A;  4GL6 A;  1I74 A;  3PTJ A;  1U1V A;  2Q9J A;  4JCI A;  2PW0 A;  4Q60 A;  1YM5 A;  2H9F A;  3EJX A;  1XUA A;  1IR6 A;  5HA4 A;  1SDJ A;  4K7X A;  1U1W A;  1K23 A;  2ZXO A;  1K20 A;  2AZP A;  1XUB A;  2GKJ A;  4LB0 A;  4JD7 A;  2HAW A;  2GKE A;  4JBD A;  4PY9 A;  2QB6 A;  1U0K A;  4LG3 A;  2IW4 A;  2KPT A;  3G98 A;  1GQZ A;  2QB8 A;  1QYA A;  5H2G A;  3G7K A;  4IJZ A;  2LT2 A;  4OA3 A;  1TM0 A;  4RPA A;  1WPP A;  1BWZ A;  5ANP A;  4LS9 A;  4K7G B;  2Q9H A;  1QY9 A;  4IK0 A;  4J9W A;  5M47 A;  3PVH A;  3DEV A;  2ZXR A;  1T6K A;  2EB0 A;  2PVZ A;  4J9X A;  1W62 A;  3FVE A;  1W61 A;  3EDN A;  2YMA A;  2OTN A;  4Q2H A;  3PW9 A;  5H2Y A; 
#chains in the Genus database with same CATH homology
 1S7J A;  2KW7 A;  3EKM A;  2ZVF A;  2ZXP A;  2QB7 A;  4JUU A;  3ICJ A;  3WQZ A;  4DUN A;  3W5W A;  2ENX A;  1U1X A;  1WPM A;  2MPB A;  3IGH X;  5IWE A;  4K8L A;  4GL6 A;  1I74 A;  3PTJ A;  1U1V A;  2Q9J A;  4JCI A;  2PW0 A;  4Q60 A;  1YM5 A;  2H9F A;  3EJX A;  1XUA A;  1IR6 A;  5HA4 A;  1SDJ A;  4K7X A;  1U1W A;  1K23 A;  2ZXO A;  1K20 A;  2AZP A;  1XUB A;  2GKJ A;  4LB0 A;  4JD7 A;  2HAW A;  2GKE A;  4JBD A;  4PY9 A;  2QB6 A;  1U0K A;  4LG3 A;  2IW4 A;  2KPT A;  3G98 A;  1GQZ A;  2QB8 A;  1QYA A;  5H2G A;  3G7K A;  4IJZ A;  2LT2 A;  4OA3 A;  1TM0 A;  4RPA A;  1WPP A;  1BWZ A;  5ANP A;  4LS9 A;  4K7G B;  2Q9H A;  1QY9 A;  4IK0 A;  4J9W A;  5M47 A;  3PVH A;  3DEV A;  2ZXR A;  1T6K A;  2EB0 A;  2PVZ A;  4J9X A;  1W62 A;  3FVE A;  1W61 A;  3EDN A;  2YMA A;  2OTN A;  4Q2H A;  3PW9 A;  5H2Y 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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#similar chains, but unknotted
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