3EKMA

Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap
Total Genus 86
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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
86
sequence length
287
structure length
287
Chain Sequence
GVLHFVKYHGLGNDFILVDNRDSSEPKITQEQAAKLCDRNFGVGADGVIFAMPGVNGTDYAMRIFNSDGSEPEMCGNGVRCFARFIAELENLQGKHSFTIHTGAGLIVPEIQDDGQVKVDMGTPILKAQDVPTKLSGNKGEAVVEAELVVDGVSWNVTCVSMGNPHCITFGKKGGPNLKVDDLNLPEIGPKFEHHEMFPARTNTEFVEVLSRSHLKMRVWERGAGATLACGTGACALVVAAVLEGRADRKCTVDLPGGPLEIEWKQEDNHIYMTGPAEAVFYGSALL
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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 Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.
pubmed doi rcsb
source organism Arabidopsis thaliana
molecule tags Isomerase
molecule keywords Diaminopimelate epimerase, chloroplastic
total genus 86
structure length 287
sequence length 287
chains with identical sequence B, C, D, E, F
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2008-09-19

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 3ekmA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 3ekmA01
4JBDA 4Q60A 4Q2HA 5IWEA 1W61A 1SDJA 3FVEA 1U1VA 1U1XA 1GQZA 2PW0A 2PVZA 1T6KA 1S7JA 3EDNA 1U0KA 1XUBA 5H2GA 1XUAA 4K7XA 1BWZA 4LB0A 2AZPA 2GKJA 4J9WA 1QY9A 2H9FA 3EJXA 3EKMA 2Q9HA 1QYAA 1YM5A 3G7KA 2GKEA 1U1WA 5H2YA 4JUUA 5M47A 4K8LA 4IK0A 5HA4A 4IJZA 4J9XA 4JCIA 1W62A 2Q9JA 4K7GB 2OTNA 4DUNA 4JD7A 1TM0A
chains in the Genus database with same CATH superfamily
4JBDA 4Q60A 4Q2HA 5IWEA 2PW0A 1T6KA 2EB0A 1S7JA 3G98A 2MPBA 2ZXPA 4LB0A 2QB6A 1I74A 2ZXOA 2GKJA 4J9WA 2H9FA 3W5WA 1U1WA 4JUUA 1TM0A 2LT2A 1WPMA 5H2GA 2IW4A 3ICJA 2Q9HA 2KPTA 3PTJA 4IK0A 4IJZA 4J9XA 4K7GB 2KW7A 4PY9A 4DUNA 1SDJA 1WPPA 2PVZA 1IR6A 3EDNA 4LG3A 1XUAA 3IGHX 4K7XA 2QB7A 1BWZA 2AZPA 1K20A 1QYAA 1YM5A 2ENXA 2ZXRA 2GKEA 5H2YA 5M47A 4K8LA 5ANPA 5HA4A 4JCIA 2QB8A 1W62A 2Q9JA 2OTNA 2YMAA 1W61A 3FVEA 3WQZA 1U1VA 1U1XA 1GQZA 2ZVFA 4RPAA 1K23A 1U0KA 1XUBA 4GL6A 4LS9A 3PVHA 3PW9A 4OA3A 1QY9A 3DEVA 3EJXA 3EKMA 3G7KA 2HAWA 4JD7A
chains in the Genus database with same CATH topology
4JBDA 4Q60A 4Q2HA 5IWEA 2PW0A 1T6KA 2EB0A 1S7JA 3G98A 2MPBA 2ZXPA 4LB0A 2QB6A 1I74A 2ZXOA 2GKJA 4J9WA 2H9FA 3W5WA 1U1WA 4JUUA 1TM0A 2LT2A 1WPMA 5H2GA 2IW4A 3ICJA 2Q9HA 2KPTA 3PTJA 4IK0A 4IJZA 4J9XA 4K7GB 2KW7A 4PY9A 4DUNA 1SDJA 1WPPA 2PVZA 1IR6A 3EDNA 4LG3A 1XUAA 3IGHX 4K7XA 2QB7A 1BWZA 2AZPA 1K20A 1QYAA 1YM5A 2ENXA 2ZXRA 2GKEA 5H2YA 5M47A 4K8LA 5ANPA 5HA4A 4JCIA 2QB8A 1W62A 2Q9JA 2OTNA 2YMAA 1W61A 3FVEA 3WQZA 1U1VA 1U1XA 1GQZA 2ZVFA 4RPAA 1K23A 1U0KA 1XUBA 4GL6A 4LS9A 3PVHA 3PW9A 4OA3A 1QY9A 3DEVA 3EJXA 3EKMA 3G7KA 2HAWA 4JD7A
chains in the Genus database with same CATH homology


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