5H2GA

Crystal strcuture of oxidized dapf from corynebacterium glutamicum
Total Genus 72
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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
72
sequence length
278
structure length
278
Chain Sequence
MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGILRVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLVDNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVFAGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTELEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGGEVEVQIFDDGSTLTGPSAIIALGEVQIH
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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 72
structure length 278
sequence length 278
chains with identical sequence B
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2016-10-15

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 5h2gA01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 5h2gA02
1XUAA 1GQZA 1S7JA 1BWZA 3EDNA 3EJXA 1U0KA 4JCIA 4IK0A 2H9FA 1QYAA 4DUNA 4J9XA 2Q9JA 2AZPA 4K7GB 2PVZA 2Q9HA 5H2YA 4J9WA 4JUUA 4Q2HA 5IWEA 3EKMA 3FVEA 4JBDA 1U1VA 5M47A 4LB0A 4IJZA 1QY9A 1TM0A 4K7XA 1SDJA 1W62A 1U1WA 1XUBA 2PW0A 4JD7A 1T6KA 4Q60A 5HA4A 5H2GA 1YM5A 3G7KA 2OTNA 2GKJA 1U1XA 2GKEA 4K8LA 1W61A
chains in the Genus database with same CATH superfamily
3IGHX 1S7JA 1BWZA 2ZXPA 2H9FA 1K23A 2LT2A 3FVEA 3ICJA 3PVHA 5M47A 1SDJA 2GKJA 4LG3A 1W62A 1XUBA 4JD7A 5HA4A 2QB6A 2GKEA 4K8LA 1W61A 3EJXA 3EDNA 3G98A 1U0KA 2ZXRA 2EB0A 2KW7A 2Q9HA 2ZVFA 2QB7A 1IR6A 4LB0A 1TM0A 2MPBA 1K20A 2PW0A 2KPTA 1I74A 2YMAA 1T6KA 4Q60A 2OTNA 1U1XA 1WPPA 4K7GB 5H2YA 3PW9A 4JUUA 3EKMA 4GL6A 4JBDA 4IJZA 4K7XA 1U1WA 3W5WA 2ZXOA 5H2GA 3G7KA 4PY9A 1XUAA 1GQZA 4JCIA 4IK0A 2ENXA 1QYAA 4DUNA 4J9XA 2Q9JA 2AZPA 2PVZA 4J9WA 4Q2HA 5IWEA 4LS9A 1U1VA 3DEVA 4OA3A 1QY9A 2HAWA 3PTJA 2QB8A 4RPAA 1WPMA 1YM5A 2IW4A 3WQZA 5ANPA
chains in the Genus database with same CATH topology
3IGHX 1S7JA 1BWZA 2ZXPA 2H9FA 1K23A 2LT2A 3FVEA 3ICJA 3PVHA 5M47A 1SDJA 2GKJA 4LG3A 1W62A 1XUBA 4JD7A 5HA4A 2QB6A 2GKEA 4K8LA 1W61A 3EJXA 3EDNA 3G98A 1U0KA 2ZXRA 2EB0A 2KW7A 2Q9HA 2ZVFA 2QB7A 1IR6A 4LB0A 1TM0A 2MPBA 1K20A 2PW0A 2KPTA 1I74A 2YMAA 1T6KA 4Q60A 2OTNA 1U1XA 1WPPA 4K7GB 5H2YA 3PW9A 4JUUA 3EKMA 4GL6A 4JBDA 4IJZA 4K7XA 1U1WA 3W5WA 2ZXOA 5H2GA 3G7KA 4PY9A 1XUAA 1GQZA 4JCIA 4IK0A 2ENXA 1QYAA 4DUNA 4J9XA 2Q9JA 2AZPA 2PVZA 4J9WA 4Q2HA 5IWEA 4LS9A 1U1VA 3DEVA 4OA3A 1QY9A 2HAWA 3PTJA 2QB8A 4RPAA 1WPMA 1YM5A 2IW4A 3WQZA 5ANPA
chains in the Genus database with same CATH homology


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