2GKJA

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap
Total Genus 82
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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
82
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 82
structure length 274
sequence length 274
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2006-04-02

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 2gkjA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 2gkjA01
3EKMA 4Q2HA 3EDNA 1W62A 1W61A 2Q9HA 4J9XA 2GKEA 1T6KA 5H2GA 1TM0A 4IJZA 1YM5A 1XUAA 4JUUA 4LB0A 4J9WA 5HA4A 2PVZA 1U0KA 1QY9A 1S7JA 3FVEA 5IWEA 1QYAA 1U1WA 3EJXA 4JCIA 4K8LA 2AZPA 2PW0A 4JBDA 5H2YA 1XUBA 2OTNA 2H9FA 2Q9JA 5M47A 4K7GB 4DUNA 3G7KA 1U1VA 1U1XA 1SDJA 4K7XA 4JD7A 1GQZA 2GKJA 4Q60A 1BWZA 4IK0A
chains in the Genus database with same CATH superfamily
1WPMA 3EDNA 1W61A 2QB8A 2GKEA 3PVHA 2YMAA 5H2GA 1XUAA 1U0KA 2ZXOA 2QB7A 4K8LA 2AZPA 5H2YA 2KW7A 2Q9JA 2H9FA 5M47A 2MPBA 3WQZA 3IGHX 1U1XA 1SDJA 4K7XA 5ANPA 1IR6A 3EKMA 1T6KA 1K23A 4IJZA 4GL6A 2ENXA 5HA4A 2HAWA 2PVZA 3FVEA 3EJXA 2EB0A 4K7GB 4DUNA 4RPAA 2GKJA 3PW9A 3ICJA 4LG3A 1W62A 2Q9HA 4JUUA 4LB0A 2QB6A 4J9WA 1QY9A 4JCIA 2PW0A 4JBDA 2IW4A 2ZVFA 1XUBA 4LS9A 2OTNA 3W5WA 2LT2A 1I74A 1GQZA 2ZXRA 1BWZA 3G98A 4OA3A 4Q2HA 4J9XA 1WPPA 1TM0A 1YM5A 1S7JA 1K20A 5IWEA 1QYAA 1U1WA 3G7KA 1U1VA 2KPTA 4PY9A 2ZXPA 4JD7A 3DEVA 4Q60A 3PTJA 4IK0A
chains in the Genus database with same CATH topology
1WPMA 3EDNA 1W61A 2QB8A 2GKEA 3PVHA 2YMAA 5H2GA 1XUAA 1U0KA 2ZXOA 2QB7A 4K8LA 2AZPA 5H2YA 2KW7A 2Q9JA 2H9FA 5M47A 2MPBA 3WQZA 3IGHX 1U1XA 1SDJA 4K7XA 5ANPA 1IR6A 3EKMA 1T6KA 1K23A 4IJZA 4GL6A 2ENXA 5HA4A 2HAWA 2PVZA 3FVEA 3EJXA 2EB0A 4K7GB 4DUNA 4RPAA 2GKJA 3PW9A 3ICJA 4LG3A 1W62A 2Q9HA 4JUUA 4LB0A 2QB6A 4J9WA 1QY9A 4JCIA 2PW0A 4JBDA 2IW4A 2ZVFA 1XUBA 4LS9A 2OTNA 3W5WA 2LT2A 1I74A 1GQZA 2ZXRA 1BWZA 3G98A 4OA3A 4Q2HA 4J9XA 1WPPA 1TM0A 1YM5A 1S7JA 1K20A 5IWEA 1QYAA 1U1WA 3G7KA 1U1VA 2KPTA 4PY9A 2ZXPA 4JD7A 3DEVA 4Q60A 3PTJA 4IK0A
chains in the Genus database with same CATH homology


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

 
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