3EJXA

Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap
Total Genus 80
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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
80
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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molecule tags Isomerase
molecule keywords Diaminopimelate epimerase, chloroplastic
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
total genus 80
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 2008-09-18

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 3ejxA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 3ejxA01
4K7GB 4K7XA 3EJXA 4Q60A 1XUAA 4IJZA 2GKJA 1U1WA 4IK0A 4K8LA 4JUUA 4DUNA 1T6KA 4LB0A 2Q9JA 1U1VA 4J9WA 4JBDA 2GKEA 4JCIA 2PW0A 1W62A 2AZPA 3EKMA 1BWZA 1S7JA 2OTNA 4J9XA 1SDJA 5H2YA 3G7KA 5H2GA 2H9FA 5M47A 1XUBA 1U1XA 5HA4A 1U0KA 3EDNA 5IWEA 1YM5A 3FVEA 2Q9HA 4Q2HA 1GQZA 1W61A 4JD7A 2PVZA 1QYAA 1QY9A 1TM0A
chains in the Genus database with same CATH superfamily
2KW7A 4LG3A 2GKJA 5ANPA 4K8LA 2LT2A 2ZXPA 3WQZA 1U1VA 2IW4A 2PW0A 3EKMA 2QB6A 2OTNA 5H2GA 5M47A 1I74A 2Q9HA 2ZVFA 1GQZA 4LS9A 1WPPA 4K7XA 1U1WA 4DUNA 4PY9A 1W62A 1BWZA 5H2YA 3G7KA 2QB7A 5HA4A 2MPBA 1U0KA 2QB8A 3EDNA 1YM5A 4JD7A 2PVZA 2HAWA 1QY9A 1TM0A 4Q2HA 4Q60A 4IJZA 4IK0A 3PVHA 4LB0A 2Q9JA 4OA3A 4J9WA 1K20A 4JCIA 2AZPA 4RPAA 2ZXOA 1SDJA 3IGHX 1XUBA 1U1XA 3W5WA 1K23A 3ICJA 5IWEA 3FVEA 1QYAA 3G98A 4K7GB 3EJXA 1IR6A 1XUAA 2KPTA 1WPMA 4JUUA 1T6KA 3PTJA 4JBDA 2GKEA 1S7JA 4J9XA 2EB0A 2H9FA 2ZXRA 3PW9A 2ENXA 1W61A 3DEVA 4GL6A 2YMAA
chains in the Genus database with same CATH topology
2KW7A 4LG3A 2GKJA 5ANPA 4K8LA 2LT2A 2ZXPA 3WQZA 1U1VA 2IW4A 2PW0A 3EKMA 2QB6A 2OTNA 5H2GA 5M47A 1I74A 2Q9HA 2ZVFA 1GQZA 4LS9A 1WPPA 4K7XA 1U1WA 4DUNA 4PY9A 1W62A 1BWZA 5H2YA 3G7KA 2QB7A 5HA4A 2MPBA 1U0KA 2QB8A 3EDNA 1YM5A 4JD7A 2PVZA 2HAWA 1QY9A 1TM0A 4Q2HA 4Q60A 4IJZA 4IK0A 3PVHA 4LB0A 2Q9JA 4OA3A 4J9WA 1K20A 4JCIA 2AZPA 4RPAA 2ZXOA 1SDJA 3IGHX 1XUBA 1U1XA 3W5WA 1K23A 3ICJA 5IWEA 3FVEA 1QYAA 3G98A 4K7GB 3EJXA 1IR6A 1XUAA 2KPTA 1WPMA 4JUUA 1T6KA 3PTJA 4JBDA 2GKEA 1S7JA 4J9XA 2EB0A 2H9FA 2ZXRA 3PW9A 2ENXA 1W61A 3DEVA 4GL6A 2YMAA
chains in the Genus database with same CATH homology


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