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


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