2GKEA

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap
Total Genus 80
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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
80
sequence length
274
structure length
274
Chain Sequence
MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHYRIFNADGSEVSQCGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQACGSGACAAVAVGIMQGLLNNNVQVDLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL
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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 Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target.
pubmed doi rcsb
source organism Haemophilus influenzae
molecule tags Isomerase
molecule keywords Diaminopimelate epimerase
total genus 80
structure length 274
sequence length 274
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2006-04-01

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01678 DAP_epimerase Diaminopimelate epimerase
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 2gkeA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 2gkeA01
4J9WA 4IK0A 2PW0A 2Q9HA 1BWZA 2GKEA 3FVEA 4JD7A 1XUAA 1S7JA 2GKJA 1GQZA 5HA4A 2AZPA 1QYAA 4IJZA 5H2YA 2Q9JA 1YM5A 2H9FA 5IWEA 4Q2HA 3EKMA 1U1VA 4DUNA 1U1XA 1U0KA 4JUUA 4K7XA 2OTNA 1TM0A 1SDJA 2PVZA 5M47A 4K8LA 5H2GA 1T6KA 4LB0A 1W62A 4J9XA 1U1WA 1XUBA 4K7GB 4JCIA 1W61A 3EDNA 4JBDA 4Q60A 3G7KA 1QY9A 3EJXA
chains in the Genus database with same CATH superfamily
4JD7A 1S7JA 1GQZA 5HA4A 2AZPA 1QYAA 3PTJA 4LS9A 4PY9A 2YMAA 1IR6A 5IWEA 4LG3A 4RPAA 2HAWA 3IGHX 4K7XA 1TM0A 1SDJA 2PVZA 4K8LA 3W5WA 1T6KA 5H2GA 1W62A 1XUBA 4K7GB 4JCIA 1W61A 1WPPA 2KPTA 3EJXA 3ICJA 4IK0A 2PW0A 2Q9HA 1XUAA 4OA3A 1I74A 2ENXA 1K20A 3DEVA 3PW9A 1K23A 3EKMA 1U1XA 3PVHA 1U0KA 4JUUA 5M47A 4J9XA 2ZXRA 2QB6A 2ZXOA 1WPMA 2EB0A 3G7KA 2KW7A 1QY9A 3G98A 4J9WA 1BWZA 2GKEA 3FVEA 5H2YA 2Q9JA 4Q2HA 1U1VA 2ZXPA 2QB7A 2OTNA 2IW4A 1U1WA 2LT2A 2ZVFA 2GKJA 4IJZA 1YM5A 2H9FA 4DUNA 4GL6A 4LB0A 2MPBA 3EDNA 4JBDA 5ANPA 3WQZA 2QB8A 4Q60A
chains in the Genus database with same CATH topology
4JD7A 1S7JA 1GQZA 5HA4A 2AZPA 1QYAA 3PTJA 4LS9A 4PY9A 2YMAA 1IR6A 5IWEA 4LG3A 4RPAA 2HAWA 3IGHX 4K7XA 1TM0A 1SDJA 2PVZA 4K8LA 3W5WA 1T6KA 5H2GA 1W62A 1XUBA 4K7GB 4JCIA 1W61A 1WPPA 2KPTA 3EJXA 3ICJA 4IK0A 2PW0A 2Q9HA 1XUAA 4OA3A 1I74A 2ENXA 1K20A 3DEVA 3PW9A 1K23A 3EKMA 1U1XA 3PVHA 1U0KA 4JUUA 5M47A 4J9XA 2ZXRA 2QB6A 2ZXOA 1WPMA 2EB0A 3G7KA 2KW7A 1QY9A 3G98A 4J9WA 1BWZA 2GKEA 3FVEA 5H2YA 2Q9JA 4Q2HA 1U1VA 2ZXPA 2QB7A 2OTNA 2IW4A 1U1WA 2LT2A 2ZVFA 2GKJA 4IJZA 1YM5A 2H9FA 4DUNA 4GL6A 4LB0A 2MPBA 3EDNA 4JBDA 5ANPA 3WQZA 2QB8A 4Q60A
chains in the Genus database with same CATH homology


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