4OX5A

Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition
Total Genus 56
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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
56
sequence length
186
structure length
184
Chain Sequence
GSHMEVVNKGDYYSIQGKYDEIIVANKHYPLSKDYNPGENPTAKAELVKLIKAMQEAGFPISDHYSGFRSYETQTKLYQDYVNGKEAADRYSARPGYSEHQTGLAFDVIGTDGDLVTEEKAAQWLLDHAADYGFVVRYLKGKEKETGYMAEEWHLRYVGKEAKEIAESGLSLEEYYGFEGGDYV
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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 Hydrolase
molecule keywords LdcB LD-carboxypeptidase
publication title Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition.
pubmed doi rcsb
source organism Streptococcus pneumoniae
total genus 56
structure length 184
sequence length 186
ec nomenclature
pdb deposition date 2014-02-04

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02557 VanY D-alanyl-D-alanine carboxypeptidase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1380.10 Alpha Beta 2-Layer Sandwich Muramoyl-pentapeptide Carboxypeptidase; domain 2 Muramoyl-pentapeptide Carboxypeptidase; domain 2 4ox5A00
2IBGE 4C4NA 4F78A 4MUQA 4OX3A 4OAKA 2WFXA 1U10A 5HNMA 2WFRA 3N1FA 4C4MA 3D1MA 4MUTA 2WG4A 4MPHA 4MUSA 3K7JB 3K7HB 1LBUA 3N1OA 3N1PB 4JIDA 1VHHA 3N1MB 4NT9A 1TZPA 2WFQA 3N1QA 2WG3A 3MXWA 4D0YA 2VO9A 3K7IB 3N1RA 3HO5H 3K7GB 3M1NA 1R44A 4OXDA 4OX5A 4MURA 3N1GA
chains in the Genus database with same CATH superfamily
2IBGE 4C4NA 4F78A 4MUQA 2BJNA 4OX3A 4OAKA 3NJCA 2WFXA 1U10A 5HNMA 2WFRA 3N1FA 2OSDA 4C4MA 3D1MA 4MUTA 1WC8A 2WG4A 2J3TA 2J3WD 4MPHA 3N1GA 4MUSA 3K7JB 3K7HB 1LBUA 3N1OA 3N1PB 2J3TB 2OSOA 4JIDA 1VHHA 2CFHA 3N1MB 2C0JA 1TZPA 4NT9A 1SZ7A 2WFQA 2CFHC 3N1QA 2WG3A 3CUEB 3MXWA 4D0YA 2C0JB 2VO9A 3K7IB 2PWNA 3N1RA 3HO5H 3K7GB 3M1NA 1R44A 4OXDA 2J3RA 4OX5A 4MURA 3CUED 2J3RB 3KXCA 2J3WB 1WC9A 3KXCC
chains in the Genus database with same CATH topology
2IBGE 4C4NA 4F78A 4MUQA 4OX3A 4OAKA 2WFXA 1U10A 5HNMA 2WFRA 3N1FA 4C4MA 3D1MA 4MUTA 2WG4A 4MPHA 4MUSA 3K7JB 3K7HB 1LBUA 3N1OA 3N1PB 4JIDA 1VHHA 3N1MB 4NT9A 1TZPA 2WFQA 3N1QA 2WG3A 3MXWA 4D0YA 2VO9A 3K7IB 3N1RA 3HO5H 3K7GB 3M1NA 1R44A 4OXDA 4OX5A 4MURA 3N1GA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2IBG E;  4C4N A;  4F78 A;  4MUQ A;  4OX3 A;  4OAK A;  2WFX A;  1U10 A;  5HNM A;  2WFR A;  3N1F A;  4C4M A;  3D1M A;  4MUT A;  2WG4 A;  4MPH A;  4MUS A;  3K7J B;  3K7H B;  1LBU A;  3N1O A;  3N1P B;  4JID A;  1VHH A;  3N1M B;  4NT9 A;  1TZP A;  2WFQ A;  3N1Q A;  2WG3 A;  3MXW A;  4D0Y A;  2VO9 A;  3K7I B;  3N1R A;  3HO5 H;  3K7G B;  3M1N A;  1R44 A;  4OXD A;  4OX5 A;  4MUR A;  3N1G A; 
#chains in the Genus database with same CATH topology
 2IBG E;  4C4N A;  4F78 A;  4MUQ A;  2BJN A;  4OX3 A;  4OAK A;  3NJC A;  2WFX A;  1U10 A;  5HNM A;  2WFR A;  3N1F A;  2OSD A;  4C4M A;  3D1M A;  4MUT A;  1WC8 A;  2WG4 A;  2J3T A;  2J3W D;  4MPH A;  3N1G A;  4MUS A;  3K7J B;  3K7H B;  1LBU A;  3N1O A;  3N1P B;  2J3T B;  2OSO A;  4JID A;  1VHH A;  2CFH A;  3N1M B;  2C0J A;  1TZP A;  4NT9 A;  1SZ7 A;  2WFQ A;  2CFH C;  3N1Q A;  2WG3 A;  3CUE B;  3MXW A;  4D0Y A;  2C0J B;  2VO9 A;  3K7I B;  2PWN A;  3N1R A;  3HO5 H;  3K7G B;  3M1N A;  1R44 A;  4OXD A;  2J3R A;  4OX5 A;  4MUR A;  3CUE D;  2J3R B;  3KXC A;  2J3W B;  1WC9 A;  3KXC C; 
#chains in the Genus database with same CATH homology
 2IBG E;  4C4N A;  4F78 A;  4MUQ A;  4OX3 A;  4OAK A;  2WFX A;  1U10 A;  5HNM A;  2WFR A;  3N1F A;  4C4M A;  3D1M A;  4MUT A;  2WG4 A;  4MPH A;  4MUS A;  3K7J B;  3K7H B;  1LBU A;  3N1O A;  3N1P B;  4JID A;  1VHH A;  3N1M B;  4NT9 A;  1TZP A;  2WFQ A;  3N1Q A;  2WG3 A;  3MXW A;  4D0Y A;  2VO9 A;  3K7I B;  3N1R A;  3HO5 H;  3K7G B;  3M1N A;  1R44 A;  4OXD A;  4OX5 A;  4MUR A;  3N1G 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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