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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molecule keywords Diaminopimelate epimerase
publication title Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target.
pubmed doi rcsb
source organism Haemophilus influenzae
molecule tags Isomerase
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
5M47A 3EJXA 4K8LA 2OTNA 1XUAA 2AZPA 5HA4A 1W61A 1U1XA 4JUUA 3EDNA 1W62A 1SDJA 3FVEA 2Q9JA 4JCIA 2GKJA 1U0KA 1YM5A 2GKEA 4JD7A 4Q2HA 5H2YA 4JBDA 2Q9HA 1T6KA 4K7XA 1U1VA 1XUBA 1TM0A 4DUNA 3G7KA 1S7JA 4IK0A 1BWZA 4J9WA 5H2GA 4LB0A 4J9XA 4Q60A 1QY9A 5IWEA 4IJZA 2PVZA 2H9FA 2PW0A 4K7GB 3EKMA 1QYAA 1U1WA 1GQZA
chains in the Genus database with same CATH superfamily
3EJXA 4K8LA 3WQZA 2MPBA 1U1XA 3IGHX 1I74A 1W62A 3G98A 5H2YA 1U1VA 1XUBA 3G7KA 3DEVA 1S7JA 4OA3A 1WPMA 1QY9A 4IJZA 2ZXRA 2PW0A 2YMAA 4LG3A 5M47A 2OTNA 5HA4A 3PVHA 2KPTA 4JUUA 3FVEA 1U0KA 2GKJA 2HAWA 2GKEA 3ICJA 3PTJA 4DUNA 5H2GA 4RPAA 1IR6A 1WPPA 2PVZA 2H9FA 4K7GB 4PY9A 1K23A 2LT2A 1SDJA 2Q9JA 3PW9A 2QB7A 4K7XA 1TM0A 2EB0A 4IK0A 4J9WA 4J9XA 4Q60A 5IWEA 2ZXPA 2IW4A 1QYAA 1XUAA 4JBDA 1U1WA 4GL6A 3W5WA 2AZPA 2QB6A 5ANPA 1W61A 1K20A 2ZVFA 3EDNA 2KW7A 4JCIA 4LS9A 1YM5A 4JD7A 4Q2HA 2Q9HA 1T6KA 2QB8A 1BWZA 4LB0A 2ENXA 3EKMA 2ZXOA 1GQZA
chains in the Genus database with same CATH topology
3EJXA 4K8LA 3WQZA 2MPBA 1U1XA 3IGHX 1I74A 1W62A 3G98A 5H2YA 1U1VA 1XUBA 3G7KA 3DEVA 1S7JA 4OA3A 1WPMA 1QY9A 4IJZA 2ZXRA 2PW0A 2YMAA 4LG3A 5M47A 2OTNA 5HA4A 3PVHA 2KPTA 4JUUA 3FVEA 1U0KA 2GKJA 2HAWA 2GKEA 3ICJA 3PTJA 4DUNA 5H2GA 4RPAA 1IR6A 1WPPA 2PVZA 2H9FA 4K7GB 4PY9A 1K23A 2LT2A 1SDJA 2Q9JA 3PW9A 2QB7A 4K7XA 1TM0A 2EB0A 4IK0A 4J9WA 4J9XA 4Q60A 5IWEA 2ZXPA 2IW4A 1QYAA 1XUAA 4JBDA 1U1WA 4GL6A 3W5WA 2AZPA 2QB6A 5ANPA 1W61A 1K20A 2ZVFA 3EDNA 2KW7A 4JCIA 4LS9A 1YM5A 4JD7A 4Q2HA 2Q9HA 1T6KA 2QB8A 1BWZA 4LB0A 2ENXA 3EKMA 2ZXOA 1GQZA
chains in the Genus database with same CATH homology


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