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 |
170
|
sequence length |
584
|
structure length |
573
|
Chain Sequence |
SIEQQLTELRTTLRHHEYLYHVMDAPEIPDAEYDRLMRELRELETKHPELITPDSPTQRPLAAFSQIRHEVPMLSLDNVFDEESFLAFNKRVQDRTWCCELKLDGLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEVRGEVFLPQAGFEKINEDARRTGGKVFANPRNAAAGSLRQLDPRITAKRPLTFFCYGVGVLEGGELPDTHLGRLLQFKKWGLPVSDRVTLCESAEEVLAFYHKVEEDRPTLGFDIDGVVIKVNSLAQQEQLGFVARAPRWAVAFKFPAQEQMTFVRDVEFQVGRTGAITPVARLEPVHVAGVLVSNATLHNADEIERLGLRIGDKVVIRRAGDVIPQVVNVVLSERPEDTREVVFPTHCPVCGSDVERVEGEAVARCTGGLICGAQRKESLKHFVSRRAMDVDGMGDKIIDQLVEKEYVHTPADLFKLTAGKLTGLERMGPKSAQNVVNALEKAKETTFARFLYALGIREVGEATAAGLAAYFGTLEALEAASIEELQKVPDVGIVVASHVHNFFAEESNRNVISELLAEGVHWPAP
|
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.
| molecule keywords |
DNA (26-MER)
|
| publication title |
Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity.
pubmed doi rcsb |
| source organism |
Escherichia coli
|
| molecule tags |
Ligase/ligase inhibitor/dna
|
| total genus |
170
|
| structure length |
573
|
| sequence length |
584
|
| ec nomenclature |
ec
6.5.1.2: DNA ligase (NAD(+)). |
| pdb deposition date | 2012-08-15 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF01653 | DNA_ligase_aden | NAD-dependent DNA ligase adenylation domain |
| A | PF03119 | DNA_ligase_ZBD | NAD-dependent DNA ligase C4 zinc finger domain |
| A | PF03120 | DNA_ligase_OB | NAD-dependent DNA ligase OB-fold domain |
| A | PF14520 | HHH_5 | Helix-hairpin-helix domain |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Alpha | Orthogonal Bundle | DNA polymerase; domain 1 | 5' to 3' exonuclease, C-terminal subdomain | ||
| Mainly Alpha | Orthogonal Bundle | DNA polymerase; domain 1 | 5' to 3' exonuclease, C-terminal subdomain | ||
| Mainly Alpha | Orthogonal Bundle | Helix Hairpins | Helix hairpin bin | ||
| Mainly Beta | Single Sheet | Ubiquitin Ligase Nedd4; Chain: W; | Ubiquitin Ligase Nedd4; Chain: W; | ||
| Mainly Beta | Beta Barrel | OB fold (Dihydrolipoamide Acetyltransferase, E2P) | Nucleic acid-binding proteins | ||
| Alpha Beta | 2-Layer Sandwich | D-amino Acid Aminotransferase; Chain A, domain 1 | DNA ligase/mRNA capping enzyme | ||
| Alpha Beta | 2-Layer Sandwich | Dna Ligase; domain 1 | Dna Ligase; domain 1 |
