2GKJA

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap
Total Genus 82
Loading diagram...

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...