2Q9JA

Crystal structure of the c217s mutant of diaminopimelate epimerase
Total Genus 70
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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
70
sequence length
274
structure length
273
Chain Sequence
MQFSKMHGLGNDFVVVDGVTQNVFFTPETIRRLANRHCGIGFDQLLIVEAPYDPELDFHYRIFNADGSEVSQGNGARCFARFVTLKGLTNKKDISVSTQKGNMVLTVKDDNQIRVNMGEPIWEPAKIPFTANKFEKNYILRTDIQTVLCGAVSMGNPHCVVQVDDIQTANVEQLGPLLESHERFPERVNAGFMQIINKEHIKLRVYERGAGETQASGSGACAAVAVGIMQGLLNNNVQVDLPGGSLMIEWNGVGHPLYMTGEATHIYDGFITL
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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
publication title Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.
pubmed doi rcsb
source organism Haemophilus influenzae
total genus 70
structure length 273
sequence length 274
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2007-06-12

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 2q9jA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 2q9jA01
1TM0A 1U1XA 1U1WA 3EDNA 4Q60A 1YM5A 5IWEA 2AZPA 4DUNA 4LB0A 5M47A 2GKJA 4Q2HA 4K8LA 4JBDA 1BWZA 1SDJA 4J9XA 1S7JA 1XUBA 3G7KA 4JUUA 2PW0A 2OTNA 4JCIA 3EJXA 5H2GA 4IJZA 3FVEA 4K7GB 4K7XA 1W62A 1XUAA 1U1VA 2GKEA 2Q9JA 4J9WA 2PVZA 3EKMA 1QY9A 1QYAA 1W61A 1T6KA 2H9FA 1U0KA 5H2YA 2Q9HA 5HA4A 4IK0A 1GQZA 4JD7A
chains in the Genus database with same CATH superfamily
2ZXOA 2ZVFA 1U1WA 4Q60A 1YM5A 2GKJA 4K8LA 2MPBA 1SDJA 4RPAA 4IJZA 3FVEA 2LT2A 2KPTA 2GKEA 2Q9JA 1W61A 4IK0A 2QB6A 1TM0A 2YMAA 3G98A 1U1XA 2AZPA 4DUNA 4J9XA 3G7KA 2PW0A 2ZXRA 3EJXA 1I74A 4K7GB 4K7XA 1U1VA 3PTJA 4J9WA 2PVZA 3EKMA 4OA3A 4LG3A 3IGHX 2ZXPA 2Q9HA 1GQZA 2QB8A 3EDNA 5IWEA 1IR6A 4LB0A 4LS9A 4Q2HA 4JBDA 1BWZA 2QB7A 1XUBA 2IW4A 4JCIA 2EB0A 5H2GA 1K23A 2ENXA 1XUAA 1QYAA 1T6KA 5H2YA 3DEVA 4JD7A 2HAWA 5ANPA 3W5WA 2KW7A 1K20A 1S7JA 1WPPA 4JUUA 1WPMA 2OTNA 4PY9A 3PVHA 4GL6A 3ICJA 3PW9A 1W62A 1QY9A 2H9FA 1U0KA 5HA4A 5M47A 3WQZA
chains in the Genus database with same CATH topology
2ZXOA 2ZVFA 1U1WA 4Q60A 1YM5A 2GKJA 4K8LA 2MPBA 1SDJA 4RPAA 4IJZA 3FVEA 2LT2A 2KPTA 2GKEA 2Q9JA 1W61A 4IK0A 2QB6A 1TM0A 2YMAA 3G98A 1U1XA 2AZPA 4DUNA 4J9XA 3G7KA 2PW0A 2ZXRA 3EJXA 1I74A 4K7GB 4K7XA 1U1VA 3PTJA 4J9WA 2PVZA 3EKMA 4OA3A 4LG3A 3IGHX 2ZXPA 2Q9HA 1GQZA 2QB8A 3EDNA 5IWEA 1IR6A 4LB0A 4LS9A 4Q2HA 4JBDA 1BWZA 2QB7A 1XUBA 2IW4A 4JCIA 2EB0A 5H2GA 1K23A 2ENXA 1XUAA 1QYAA 1T6KA 5H2YA 3DEVA 4JD7A 2HAWA 5ANPA 3W5WA 2KW7A 1K20A 1S7JA 1WPPA 4JUUA 1WPMA 2OTNA 4PY9A 3PVHA 4GL6A 3ICJA 3PW9A 1W62A 1QY9A 2H9FA 1U0KA 5HA4A 5M47A 3WQZA
chains in the Genus database with same CATH homology


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

 
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