1SDJA

X-ray structure of ydde_ecoli northeast structural genomics consortium target et25.
Total Genus 72
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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
72
sequence length
310
structure length
310
Chain Sequence
SGRENLYFQGHMKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIELGS
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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 Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Structural genomics, unknown function
molecule keywords Hypothetical protein yddE
total genus 72
structure length 310
sequence length 310
ec nomenclature
pdb deposition date 2004-02-13

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 1sdjA01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 1sdjA02
2OTNA 3EKMA 1XUAA 4Q2HA 5H2GA 1S7JA 1YM5A 4K8LA 1QYAA 2AZPA 4IJZA 5H2YA 1T6KA 4DUNA 3EDNA 4J9WA 4J9XA 4LB0A 2Q9HA 4IK0A 5M47A 1BWZA 1SDJA 5HA4A 1GQZA 3FVEA 4JCIA 3G7KA 1XUBA 2PW0A 4JUUA 2GKEA 1TM0A 2GKJA 1U0KA 1U1XA 4JBDA 5IWEA 1U1WA 3EJXA 4K7GB 4K7XA 2Q9JA 4JD7A 4Q60A 1W62A 1W61A 2PVZA 1QY9A 2H9FA 1U1VA
chains in the Genus database with same CATH superfamily
1S7JA 1YM5A 1QYAA 2EB0A 4LB0A 5M47A 1BWZA 1SDJA 5HA4A 1WPMA 4OA3A 4JUUA 4JBDA 1U1WA 4K7XA 3PW9A 2HAWA 1W62A 1QY9A 2H9FA 3IGHX 3DEVA 4IJZA 1T6KA 2ZXOA 3ICJA 2QB6A 4J9WA 3WQZA 2Q9HA 4LG3A 3PVHA 5ANPA 1GQZA 2ZVFA 2GKEA 1TM0A 1K23A 4K7GB 3PTJA 4JD7A 1W61A 2PVZA 2OTNA 1XUAA 4Q2HA 5H2GA 4LS9A 2MPBA 5H2YA 1WPPA 2YMAA 2LT2A 3EDNA 4J9XA 2KPTA 4GL6A 4IK0A 4RPAA 2ZXPA 2ZXRA 4JCIA 2KW7A 2IW4A 3W5WA 3G7KA 2PW0A 2GKJA 1U0KA 1U1XA 2Q9JA 1K20A 4Q60A 3EKMA 2QB8A 3G98A 4K8LA 2AZPA 2ENXA 1IR6A 4PY9A 3FVEA 1I74A 2QB7A 1XUBA 5IWEA 3EJXA 4DUNA 1U1VA
chains in the Genus database with same CATH topology
1S7JA 1YM5A 1QYAA 2EB0A 4LB0A 5M47A 1BWZA 1SDJA 5HA4A 1WPMA 4OA3A 4JUUA 4JBDA 1U1WA 4K7XA 3PW9A 2HAWA 1W62A 1QY9A 2H9FA 3IGHX 3DEVA 4IJZA 1T6KA 2ZXOA 3ICJA 2QB6A 4J9WA 3WQZA 2Q9HA 4LG3A 3PVHA 5ANPA 1GQZA 2ZVFA 2GKEA 1TM0A 1K23A 4K7GB 3PTJA 4JD7A 1W61A 2PVZA 2OTNA 1XUAA 4Q2HA 5H2GA 4LS9A 2MPBA 5H2YA 1WPPA 2YMAA 2LT2A 3EDNA 4J9XA 2KPTA 4GL6A 4IK0A 4RPAA 2ZXPA 2ZXRA 4JCIA 2KW7A 2IW4A 3W5WA 3G7KA 2PW0A 2GKJA 1U0KA 1U1XA 2Q9JA 1K20A 4Q60A 3EKMA 2QB8A 3G98A 4K8LA 2AZPA 2ENXA 1IR6A 4PY9A 3FVEA 1I74A 2QB7A 1XUBA 5IWEA 3EJXA 4DUNA 1U1VA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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