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


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