4IJZA

Crystal structure of diaminopimelate epimerase from escherichia coli
Total Genus 75
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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
75
sequence length
274
structure length
274
Chain Sequence
MQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL
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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 Dimerization of bacterial diaminopimelate epimerase is essential for catalysis
pubmed doi rcsb
source organism Escherichia coli
molecule tags Isomerase
molecule keywords Diaminopimelate epimerase
total genus 75
structure length 274
sequence length 274
chains with identical sequence B
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2012-12-24

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 4ijzA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 4ijzA01
4Q60A 3EDNA 4IK0A 1W61A 4JD7A 4Q2HA 2GKEA 1SDJA 1W62A 2OTNA 1BWZA 1YM5A 4JCIA 3FVEA 1T6KA 2PVZA 4LB0A 1XUAA 4IJZA 3EJXA 1U1VA 4DUNA 5M47A 1TM0A 4JUUA 2PW0A 4K7XA 1S7JA 2Q9JA 4J9WA 1U0KA 1U1XA 1QYAA 5H2GA 5HA4A 4J9XA 3EKMA 3G7KA 1XUBA 1QY9A 4K7GB 1U1WA 2Q9HA 4K8LA 2AZPA 4JBDA 5IWEA 1GQZA 2H9FA 2GKJA 5H2YA
chains in the Genus database with same CATH superfamily
2HAWA 4IK0A 4Q2HA 1BWZA 2PVZA 1XUAA 4DUNA 2PW0A 1U0KA 5H2GA 3EKMA 3ICJA 2KPTA 2Q9HA 4K8LA 3W5WA 2AZPA 2QB6A 4JBDA 1GQZA 2H9FA 2ZXPA 2YMAA 1SDJA 2KW7A 3PVHA 3G98A 4LB0A 4OA3A 1TM0A 4JUUA 2ZXOA 1S7JA 2Q9JA 1WPPA 4RPAA 3PW9A 4K7GB 1K23A 1K20A 2EB0A 5IWEA 1WPMA 5H2YA 2ZXRA 4Q60A 4JD7A 1W61A 2GKEA 1W62A 2OTNA 4JCIA 4LS9A 3FVEA 2MPBA 4IJZA 3EJXA 5M47A 2ZVFA 4K7XA 4J9WA 1U1XA 1QYAA 4PY9A 5HA4A 4J9XA 3PTJA 1IR6A 1U1WA 2ENXA 2GKJA 3DEVA 3EDNA 4LG3A 2QB7A 1YM5A 5ANPA 1T6KA 1U1VA 2QB8A 3G7KA 1XUBA 1QY9A 1I74A 2IW4A 3WQZA 4GL6A 3IGHX 2LT2A
chains in the Genus database with same CATH topology
2HAWA 4IK0A 4Q2HA 1BWZA 2PVZA 1XUAA 4DUNA 2PW0A 1U0KA 5H2GA 3EKMA 3ICJA 2KPTA 2Q9HA 4K8LA 3W5WA 2AZPA 2QB6A 4JBDA 1GQZA 2H9FA 2ZXPA 2YMAA 1SDJA 2KW7A 3PVHA 3G98A 4LB0A 4OA3A 1TM0A 4JUUA 2ZXOA 1S7JA 2Q9JA 1WPPA 4RPAA 3PW9A 4K7GB 1K23A 1K20A 2EB0A 5IWEA 1WPMA 5H2YA 2ZXRA 4Q60A 4JD7A 1W61A 2GKEA 1W62A 2OTNA 4JCIA 4LS9A 3FVEA 2MPBA 4IJZA 3EJXA 5M47A 2ZVFA 4K7XA 4J9WA 1U1XA 1QYAA 4PY9A 5HA4A 4J9XA 3PTJA 1IR6A 1U1WA 2ENXA 2GKJA 3DEVA 3EDNA 4LG3A 2QB7A 1YM5A 5ANPA 1T6KA 1U1VA 2QB8A 3G7KA 1XUBA 1QY9A 1I74A 2IW4A 3WQZA 4GL6A 3IGHX 2LT2A
chains in the Genus database with same CATH homology


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