1QYAA

Crystal structure of e. coli protein ydde
Total Genus 82
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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
82
sequence length
297
structure length
293
Chain Sequence
LKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPIHATVAAHYVRAKVLGLGNCTIWQTSLKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL
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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 HYPOTHETICAL PROTEIN yddE
publication title Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase
pubmed doi rcsb
source organism Escherichia coli
total genus 82
structure length 293
sequence length 297
chains with identical sequence B
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 1qyaA01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 1qyaA02
4JUUA 2GKJA 1TM0A 1W62A 3EJXA 4J9XA 5H2YA 4IK0A 1T6KA 1SDJA 1U0KA 4K8LA 1XUAA 1U1XA 1GQZA 2Q9JA 3EKMA 2PW0A 2H9FA 4LB0A 2GKEA 4JD7A 4IJZA 5M47A 4DUNA 4Q60A 3G7KA 2OTNA 4K7GB 1XUBA 4J9WA 2AZPA 4JCIA 1W61A 5H2GA 1QY9A 4Q2HA 2Q9HA 4JBDA 1U1WA 1QYAA 1YM5A 3FVEA 5IWEA 1S7JA 1U1VA 4K7XA 2PVZA 3EDNA 1BWZA 5HA4A
chains in the Genus database with same CATH superfamily
3W5WA 1K23A 4IK0A 3PTJA 1XUAA 2GKEA 2EB0A 2ENXA 4Q60A 4K7GB 2MPBA 1W61A 5H2GA 4LS9A 2ZXRA 4GL6A 5IWEA 2PVZA 3EDNA 4J9XA 2IW4A 1TM0A 4K8LA 3EKMA 1GQZA 4RPAA 3WQZA 2H9FA 4JD7A 2KW7A 2OTNA 4LG3A 2ZXPA 4J9WA 2Q9HA 1U1WA 2LT2A 2QB8A 1YM5A 3FVEA 3DEVA 5HA4A 2GKJA 1T6KA 1SDJA 1U0KA 2Q9JA 4PY9A 1I74A 2PW0A 2ZXOA 4OA3A 2YMAA 4IJZA 2QB6A 4DUNA 2HAWA 1XUBA 2AZPA 2KPTA 4JCIA 3PW9A 1QYAA 4K7XA 5ANPA 3ICJA 1BWZA 2QB7A 3G98A 4JUUA 3PVHA 5H2YA 1W62A 3EJXA 1U1XA 3IGHX 4LB0A 2ZVFA 1IR6A 5M47A 1K20A 3G7KA 1QY9A 4Q2HA 1WPPA 4JBDA 1S7JA 1U1VA 1WPMA
chains in the Genus database with same CATH topology
3W5WA 1K23A 4IK0A 3PTJA 1XUAA 2GKEA 2EB0A 2ENXA 4Q60A 4K7GB 2MPBA 1W61A 5H2GA 4LS9A 2ZXRA 4GL6A 5IWEA 2PVZA 3EDNA 4J9XA 2IW4A 1TM0A 4K8LA 3EKMA 1GQZA 4RPAA 3WQZA 2H9FA 4JD7A 2KW7A 2OTNA 4LG3A 2ZXPA 4J9WA 2Q9HA 1U1WA 2LT2A 2QB8A 1YM5A 3FVEA 3DEVA 5HA4A 2GKJA 1T6KA 1SDJA 1U0KA 2Q9JA 4PY9A 1I74A 2PW0A 2ZXOA 4OA3A 2YMAA 4IJZA 2QB6A 4DUNA 2HAWA 1XUBA 2AZPA 2KPTA 4JCIA 3PW9A 1QYAA 4K7XA 5ANPA 3ICJA 1BWZA 2QB7A 3G98A 4JUUA 3PVHA 5H2YA 1W62A 3EJXA 1U1XA 3IGHX 4LB0A 2ZVFA 1IR6A 5M47A 1K20A 3G7KA 1QY9A 4Q2HA 1WPPA 4JBDA 1S7JA 1U1VA 1WPMA
chains in the Genus database with same CATH homology


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