5M47A

Crystal strcuture of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate
Total Genus 73
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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
73
sequence length
280
structure length
280
Chain Sequence
MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGILRVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLVDNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVFAGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTELEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGGEVEVQIFDDGSTLTGPSAIIALGEVQIHHH
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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 Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
pubmed doi rcsb
source organism Corynebacterium glutamicum (strain atcc 13032 / dsm 20300 / jcm 1318 / lmg 3730
molecule tags Isomerase
molecule keywords Diaminopimelate epimerase
total genus 73
structure length 280
sequence length 280
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2016-10-18

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 5m47A01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 5m47A02
2GKEA 3FVEA 1GQZA 3EJXA 1U1VA 2GKJA 1W62A 5HA4A 1QYAA 1BWZA 4Q2HA 1XUAA 1TM0A 1YM5A 4JBDA 4JCIA 4DUNA 4J9WA 1SDJA 1U0KA 4LB0A 1W61A 2AZPA 4K7GB 5M47A 2PVZA 4K7XA 3G7KA 2Q9JA 5IWEA 1XUBA 2OTNA 4JUUA 1U1WA 5H2GA 1S7JA 1U1XA 4Q60A 4K8LA 2PW0A 5H2YA 3EKMA 4JD7A 4IJZA 4IK0A 4J9XA 1QY9A 1T6KA 2H9FA 2Q9HA 3EDNA
chains in the Genus database with same CATH superfamily
1I74A 1U1VA 2GKJA 1K23A 1W62A 1SDJA 2ZVFA 3W5WA 4LB0A 4K7XA 4RPAA 4Q60A 2QB8A 2QB7A 2MPBA 3EKMA 4IJZA 2YMAA 2H9FA 2EB0A 3PVHA 3WQZA 3EJXA 2KPTA 5HA4A 1TM0A 1YM5A 4J9WA 2AZPA 5M47A 2LT2A 3G7KA 2OTNA 1WPPA 5H2GA 1S7JA 1U1XA 5H2YA 4JD7A 4LS9A 2Q9HA 5ANPA 2HAWA 2QB6A 1QYAA 4Q2HA 4JCIA 4JBDA 2ZXOA 1WPMA 4DUNA 1K20A 1U0KA 3G98A 2IW4A 4K7GB 2ZXPA 4JUUA 1U1WA 4K8LA 4GL6A 4OA3A 2KW7A 3PTJA 2ENXA 2GKEA 3FVEA 1GQZA 3PW9A 1BWZA 1XUAA 1W61A 4PY9A 2PVZA 3DEVA 2ZXRA 2Q9JA 5IWEA 4LG3A 1XUBA 1IR6A 3ICJA 2PW0A 3IGHX 4IK0A 4J9XA 1QY9A 1T6KA 3EDNA
chains in the Genus database with same CATH topology
1I74A 1U1VA 2GKJA 1K23A 1W62A 1SDJA 2ZVFA 3W5WA 4LB0A 4K7XA 4RPAA 4Q60A 2QB8A 2QB7A 2MPBA 3EKMA 4IJZA 2YMAA 2H9FA 2EB0A 3PVHA 3WQZA 3EJXA 2KPTA 5HA4A 1TM0A 1YM5A 4J9WA 2AZPA 5M47A 2LT2A 3G7KA 2OTNA 1WPPA 5H2GA 1S7JA 1U1XA 5H2YA 4JD7A 4LS9A 2Q9HA 5ANPA 2HAWA 2QB6A 1QYAA 4Q2HA 4JCIA 4JBDA 2ZXOA 1WPMA 4DUNA 1K20A 1U0KA 3G98A 2IW4A 4K7GB 2ZXPA 4JUUA 1U1WA 4K8LA 4GL6A 4OA3A 2KW7A 3PTJA 2ENXA 2GKEA 3FVEA 1GQZA 3PW9A 1BWZA 1XUAA 1W61A 4PY9A 2PVZA 3DEVA 2ZXRA 2Q9JA 5IWEA 4LG3A 1XUBA 1IR6A 3ICJA 2PW0A 3IGHX 4IK0A 4J9XA 1QY9A 1T6KA 3EDNA
chains in the Genus database with same CATH homology


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