1QYAA

Crystal structure of e. coli protein ydde
Total Genus 82
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
82
sequence length
297
structure length
293
Chain Sequence
b'LKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPIHATVAAHYVRAKVLGLGNCTIWQTSLKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL'
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 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
3G7KA 1U0KA 4K7XA 1QY9A 4Q2HA 3EJXA 1U1WA 5IWEA 4K8LA 4K7GB 1U1VA 3EDNA 2OTNA 2PW0A 1TM0A 1SDJA 5HA4A 5H2GA 4J9WA 4JD7A 2GKEA 5H2YA 4JBDA 4JUUA 1GQZA 2AZPA 1W61A 4LB0A 2Q9HA 4JCIA 4Q60A 1W62A 1XUAA 2Q9JA 4IK0A 4IJZA 5M47A 4J9XA 1U1XA 1BWZA 1QYAA 2GKJA 3FVEA 2PVZA 1XUBA 1YM5A 2H9FA 3EKMA 1T6KA 4DUNA 1S7JA
chains in the Genus database with same CATH superfamily
4K7XA 1U0KA 1QY9A 1K23A 2HAWA 5IWEA 4K8LA 1U1VA 3EDNA 2PW0A 3ICJA 3PW9A 4J9WA 2KPTA 1GQZA 2IW4A 4JCIA 3DEVA 4Q60A 2LT2A 2Q9JA 4IK0A 2GKJA 2MPBA 4OA3A 3G98A 3EJXA 2KW7A 3PTJA 1TM0A 5HA4A 1IR6A 1I74A 5ANPA 5H2GA 2Q9HA 2QB7A 1WPMA 1XUAA 5M47A 3W5WA 1QYAA 1XUBA 3EKMA 1T6KA 4DUNA 4Q2HA 1U1WA 2QB8A 4K7GB 2ZVFA 4JD7A 2GKEA 5H2YA 3PVHA 2AZPA 2ZXPA 4LB0A 1WPPA 2ENXA 1W62A 4LS9A 1BWZA 1YM5A 2H9FA 3G7KA 2ZXOA 1K20A 4PY9A 3IGHX 4RPAA 2EB0A 1SDJA 2ZXRA 2YMAA 4JBDA 4JUUA 3WQZA 1W61A 2QB6A 4IJZA 4J9XA 1U1XA 3FVEA 4GL6A 2PVZA 2OTNA 4LG3A 1S7JA
chains in the Genus database with same CATH topology
4K7XA 1U0KA 1QY9A 1K23A 2HAWA 5IWEA 4K8LA 1U1VA 3EDNA 2PW0A 3ICJA 3PW9A 4J9WA 2KPTA 1GQZA 2IW4A 4JCIA 3DEVA 4Q60A 2LT2A 2Q9JA 4IK0A 2GKJA 2MPBA 4OA3A 3G98A 3EJXA 2KW7A 3PTJA 1TM0A 5HA4A 1IR6A 1I74A 5ANPA 5H2GA 2Q9HA 2QB7A 1WPMA 1XUAA 5M47A 3W5WA 1QYAA 1XUBA 3EKMA 1T6KA 4DUNA 4Q2HA 1U1WA 2QB8A 4K7GB 2ZVFA 4JD7A 2GKEA 5H2YA 3PVHA 2AZPA 2ZXPA 4LB0A 1WPPA 2ENXA 1W62A 4LS9A 1BWZA 1YM5A 2H9FA 3G7KA 2ZXOA 1K20A 4PY9A 3IGHX 4RPAA 2EB0A 1SDJA 2ZXRA 2YMAA 4JBDA 4JUUA 3WQZA 1W61A 2QB6A 4IJZA 4J9XA 1U1XA 3FVEA 4GL6A 2PVZA 2OTNA 4LG3A 1S7JA
chains in the Genus database with same CATH homology


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