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


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