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 |
96
|
sequence length |
306
|
structure length |
306
|
Chain Sequence |
MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD
|
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.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
pubmed doi rcsb |
| molecule keywords |
D-alanine--D-alanine ligase
|
| molecule tags |
Ligase
|
| source organism |
Yersinia pestis
|
| total genus |
96
|
| structure length |
306
|
| sequence length |
306
|
| chains with identical sequence |
B, C, D
|
| ec nomenclature |
ec
6.3.2.4: D-alanine--D-alanine ligase. |
| pdb deposition date | 2015-05-28 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF01820 | Dala_Dala_lig_N | D-ala D-ala ligase N-terminus |
| A | PF07478 | Dala_Dala_lig_C | D-ala D-ala ligase C-terminus |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Alpha Beta | 2-Layer Sandwich | D-amino Acid Aminotransferase; Chain A, domain 1 | ATP-grasp fold, B domain | ||
| Alpha Beta | 2-Layer Sandwich | Dna Ligase; domain 1 | ATP-grasp fold, A domain | ||
| Alpha Beta | 3-Layer(aba) Sandwich | Rossmann fold | Rossmann fold |
