5H2YA

Crystal strcuture of reduced dapf from corynebacterium glutamicum
Total Genus 73
Loading diagram...

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
278
structure length
278
Chain Sequence
b'MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGILRVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLVDNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVFAGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTELEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGGEVEVQIFDDGSTLTGPSAIIALGEVQIH'
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
molecule keywords Diaminopimelate epimerase
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
total genus 73
structure length 278
sequence length 278
chains with identical sequence B
ec nomenclature ec 5.1.1.7: Diaminopimelate epimerase.
pdb deposition date 2016-10-18

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 5h2yA01
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 5h2yA02
3EDNA 4DUNA 2AZPA 4J9WA 3EKMA 5IWEA 4K8LA 4J9XA 4LB0A 3G7KA 2Q9HA 1W61A 1T6KA 1U1WA 1U1XA 2H9FA 4IK0A 4JBDA 5HA4A 2GKJA 1BWZA 1XUBA 1XUAA 2PW0A 4K7GB 1U0KA 4Q60A 5M47A 2PVZA 4Q2HA 1SDJA 4K7XA 1GQZA 5H2YA 5H2GA 3FVEA 1YM5A 2Q9JA 4JD7A 1W62A 3EJXA 1S7JA 4IJZA 1QYAA 2GKEA 2OTNA 4JUUA 1TM0A 1U1VA 1QY9A 4JCIA
chains in the Genus database with same CATH superfamily
4RPAA 3EDNA 2EB0A 2YMAA 5HA4A 1XUAA 2PW0A 2ENXA 4Q2HA 1SDJA 4K7XA 2Q9JA 3EJXA 2QB7A 2GKEA 1TM0A 1U1VA 1QY9A 1I74A 2HAWA 2ZXRA 4DUNA 3DEVA 4LS9A 2ZVFA 3G98A 2H9FA 2GKJA 4K7GB 1U0KA 1WPPA 2KPTA 5H2GA 1W62A 2QB6A 1S7JA 4JUUA 4PY9A 1K20A 2AZPA 4J9WA 1WPMA 4K8LA 4OA3A 5ANPA 3G7KA 1T6KA 4JBDA 4IK0A 3PTJA 1XUBA 4LG3A 5M47A 4Q60A 4GL6A 3FVEA 4JD7A 3PW9A 3WQZA 3W5WA 3PVHA 2LT2A 4J9XA 2ZXOA 1QYAA 2MPBA 3EKMA 5IWEA 1K23A 4LB0A 2Q9HA 1W61A 1U1WA 1U1XA 1IR6A 1BWZA 2IW4A 2QB8A 3ICJA 2PVZA 1GQZA 2ZXPA 5H2YA 1YM5A 2KW7A 3IGHX 4IJZA 2OTNA 4JCIA
chains in the Genus database with same CATH topology
4RPAA 3EDNA 2EB0A 2YMAA 5HA4A 1XUAA 2PW0A 2ENXA 4Q2HA 1SDJA 4K7XA 2Q9JA 3EJXA 2QB7A 2GKEA 1TM0A 1U1VA 1QY9A 1I74A 2HAWA 2ZXRA 4DUNA 3DEVA 4LS9A 2ZVFA 3G98A 2H9FA 2GKJA 4K7GB 1U0KA 1WPPA 2KPTA 5H2GA 1W62A 2QB6A 1S7JA 4JUUA 4PY9A 1K20A 2AZPA 4J9WA 1WPMA 4K8LA 4OA3A 5ANPA 3G7KA 1T6KA 4JBDA 4IK0A 3PTJA 1XUBA 4LG3A 5M47A 4Q60A 4GL6A 3FVEA 4JD7A 3PW9A 3WQZA 3W5WA 3PVHA 2LT2A 4J9XA 2ZXOA 1QYAA 2MPBA 3EKMA 5IWEA 1K23A 4LB0A 2Q9HA 1W61A 1U1WA 1U1XA 1IR6A 1BWZA 2IW4A 2QB8A 3ICJA 2PVZA 1GQZA 2ZXPA 5H2YA 1YM5A 2KW7A 3IGHX 4IJZA 2OTNA 4JCIA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...