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
1W61A 3EDNA 2PVZA 1QY9A 1TM0A 2Q9HA 2GKEA 3G7KA 4Q2HA 1T6KA 4LB0A 4J9XA 2AZPA 3FVEA 4K7GB 4JD7A 5H2GA 2OTNA 2PW0A 5H2YA 2GKJA 4IJZA 1SDJA 5M47A 5IWEA 4JBDA 1S7JA 1U0KA 1W62A 1U1WA 2H9FA 4J9WA 1QYAA 1U1XA 4K8LA 3EKMA 4IK0A 4K7XA 1XUBA 4DUNA 1YM5A 4JUUA 1BWZA 4Q60A 1U1VA 5HA4A 1GQZA 4JCIA 2Q9JA 1XUAA 3EJXA
chains in the Genus database with same CATH superfamily
3EDNA 3PW9A 2Q9HA 4LB0A 2KW7A 2QB7A 3FVEA 2ZXRA 5IWEA 1S7JA 1K20A 3PVHA 4GL6A 3PTJA 4LG3A 4DUNA 4JUUA 1BWZA 1WPPA 1U1VA 4Q60A 2PVZA 3IGHX 4Q2HA 2ZVFA 2ZXPA 2ENXA 5H2GA 2PW0A 2GKJA 2IW4A 2QB6A 4RPAA 1U0KA 1W62A 1U1WA 1QYAA 1U1XA 3G98A 4IK0A 1XUBA 5HA4A 1GQZA 3W5WA 2Q9JA 4JCIA 2QB8A 1K23A 2LT2A 2GKEA 3G7KA 2HAWA 1T6KA 1WPMA 1I74A 4K7GB 4JD7A 2OTNA 5H2YA 5M47A 1SDJA 4LS9A 4OA3A 4JBDA 4PY9A 2KPTA 3EJXA 2H9FA 3ICJA 4K8LA 4K7XA 1XUAA 1W61A 2EB0A 2MPBA 1TM0A 3DEVA 2AZPA 4IJZA 2YMAA 4J9WA 2ZXOA 3EKMA 3WQZA 1YM5A 1IR6A 5ANPA 1QY9A 4J9XA
chains in the Genus database with same CATH topology
3EDNA 3PW9A 2Q9HA 4LB0A 2KW7A 2QB7A 3FVEA 2ZXRA 5IWEA 1S7JA 1K20A 3PVHA 4GL6A 3PTJA 4LG3A 4DUNA 4JUUA 1BWZA 1WPPA 1U1VA 4Q60A 2PVZA 3IGHX 4Q2HA 2ZVFA 2ZXPA 2ENXA 5H2GA 2PW0A 2GKJA 2IW4A 2QB6A 4RPAA 1U0KA 1W62A 1U1WA 1QYAA 1U1XA 3G98A 4IK0A 1XUBA 5HA4A 1GQZA 3W5WA 2Q9JA 4JCIA 2QB8A 1K23A 2LT2A 2GKEA 3G7KA 2HAWA 1T6KA 1WPMA 1I74A 4K7GB 4JD7A 2OTNA 5H2YA 5M47A 1SDJA 4LS9A 4OA3A 4JBDA 4PY9A 2KPTA 3EJXA 2H9FA 3ICJA 4K8LA 4K7XA 1XUAA 1W61A 2EB0A 2MPBA 1TM0A 3DEVA 2AZPA 4IJZA 2YMAA 4J9WA 2ZXOA 3EKMA 3WQZA 1YM5A 1IR6A 5ANPA 1QY9A 4J9XA
chains in the Genus database with same CATH homology


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