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


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