1QY9A

Crystal structure of e. coli se-met protein ydde
Total Genus 77
Loading diagram...

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
Loading diagram...

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


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

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