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


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