1GVMA

Choline binding domain of the major autolysin (c-lyta) from streptococcus pneumoniae
Total Genus 14
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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
14
sequence length
127
structure length
127
Chain Sequence
GSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK
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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.

publication title Two New Crystal Forms of the Choline-Binding Domain of the Major Pneumococcal Autolysin: Insights Into the Dynamics of the Active Dimeric
pubmed doi rcsb
molecule tags Choline-binding domain
source organism Streptococcus pneumoniae
molecule keywords AUTOLYSIN
total genus 14
structure length 127
sequence length 127
chains with identical sequence B, C, D, E, F
ec nomenclature ec 3.5.1.28: N-acetylmuramoyl-L-alanine amidase.
pdb deposition date 2002-02-15

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01473 CW_binding_1 Putative cell wall binding repeat
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.10.270.10 Mainly Beta Ribbon left handed beta-beta-3-solenoid Cholin Binding 1gvmA00
3HZ3A 4X36A 3KLKA 4TVCA 2V05A 1GVMA 3HIAA 2IXUA 4NBXA 1HCXA 2G7CA 2IXVA 1OBAA 3KLLA 4NBZA 2X8OA 3TTOA 2V04A 2J8GA 4NBYA 2VYUA 4NC2A 4TVDA 2X8MA 2F6EA 3TTQA 1H09A 4NC0A 2X8PA 4AYGA 2BMLA 4TTUA 2QJ6A 2J8FA 1H8GA
chains in the Genus database with same CATH superfamily
3HZ3A 4X36A 3KLKA 4TVCA 2V05A 1GVMA 3HIAA 2IXUA 4NBXA 1HCXA 2G7CA 2IXVA 1OBAA 3KLLA 4NBZA 2X8OA 3TTOA 2V04A 2J8GA 4NBYA 2VYUA 4NC2A 4TVDA 2X8MA 2F6EA 3TTQA 1H09A 4NC0A 2X8PA 4AYGA 2BMLA 4TTUA 2QJ6A 2J8FA 1H8GA
chains in the Genus database with same CATH topology
3HZ3A 4X36A 3KLKA 4TVCA 2V05A 1GVMA 3HIAA 2IXUA 4NBXA 1HCXA 2G7CA 2IXVA 1OBAA 3KLLA 4NBZA 2X8OA 3TTOA 2V04A 2J8GA 4NBYA 2VYUA 4NC2A 4TVDA 2X8MA 2F6EA 3TTQA 1H09A 4NC0A 2X8PA 4AYGA 2BMLA 4TTUA 2QJ6A 2J8FA 1H8GA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3HZ3 A;  4X36 A;  3KLK A;  4TVC A;  2V05 A;  1GVM A;  3HIA A;  2IXU A;  4NBX A;  1HCX A;  2G7C A;  2IXV A;  1OBA A;  3KLL A;  4NBZ A;  2X8O A;  3TTO A;  2V04 A;  2J8G A;  4NBY A;  2VYU A;  4NC2 A;  4TVD A;  2X8M A;  2F6E A;  3TTQ A;  1H09 A;  4NC0 A;  2X8P A;  4AYG A;  2BML A;  4TTU A;  2QJ6 A;  2J8F A;  1H8G A; 
#chains in the Genus database with same CATH topology
 3HZ3 A;  4X36 A;  3KLK A;  4TVC A;  2V05 A;  1GVM A;  3HIA A;  2IXU A;  4NBX A;  1HCX A;  2G7C A;  2IXV A;  1OBA A;  3KLL A;  4NBZ A;  2X8O A;  3TTO A;  2V04 A;  2J8G A;  4NBY A;  2VYU A;  4NC2 A;  4TVD A;  2X8M A;  2F6E A;  3TTQ A;  1H09 A;  4NC0 A;  2X8P A;  4AYG A;  2BML A;  4TTU A;  2QJ6 A;  2J8F A;  1H8G A; 
#chains in the Genus database with same CATH homology
 3HZ3 A;  4X36 A;  3KLK A;  4TVC A;  2V05 A;  1GVM A;  3HIA A;  2IXU A;  4NBX A;  1HCX A;  2G7C A;  2IXV A;  1OBA A;  3KLL A;  4NBZ A;  2X8O A;  3TTO A;  2V04 A;  2J8G A;  4NBY A;  2VYU A;  4NC2 A;  4TVD A;  2X8M A;  2F6E A;  3TTQ A;  1H09 A;  4NC0 A;  2X8P A;  4AYG A;  2BML A;  4TTU A;  2QJ6 A;  2J8F A;  1H8G 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)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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