2FAQA

Crystal structure of pseudomonas aeruginosa ligd polymerase domain with atp and manganese
Total Genus 89
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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
89
sequence length
295
structure length
295
Chain Sequence
RAATAGVRISHPQRLIDPSIQASKLELAEFHARYADLLLRDLRERPVSLVRGPDGIGGELFFQKHAARLKIPGIVQLDPALDPGHPPLLQIRSAEALVGAVQMGSIEFHTWNASLANLERPDRFVLDLDPDPALPWKRMLEATQLSLTLLDELGLRAFLKTSGGKGMHLLVPLERRHGWDEVKDFAQAISQHLARLMPERFSAVSGPRNRVGKIFVDYLRNSRGASTVAAYSVRAREGLPVSVPVFREELDSLQGANQWNLRSLPQRLDELAGDDPWADYAGTRQRISAAMRRQL
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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 Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D
pubmed doi rcsb
molecule tags Hydrolase/transferase
source organism Pseudomonas aeruginosa
molecule keywords probable ATP-dependent DNA ligase
total genus 89
structure length 295
sequence length 295
chains with identical sequence B
ec nomenclature ec 6.5.1.1: DNA ligase (ATP).
pdb deposition date 2005-12-07
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.920.30 Alpha Beta Alpha-Beta Complex DNA primase, PRIM domain DNA primase, PRIM domain 2faqA01
4BPUA 4LIMA 4LILA 4MHQA 4BPXA 4BPWA 4MM2A 2FAOA 5EXRA 2FAQA 4LIKA 4RR2A 2FARA 1ZT2A
chains in the Genus database with same CATH superfamily
1V34A 4BPUA 4LIMA 1V33A 1G71A 4LILA 4MHQA 4BPXA 4BPWA 2FARA 4MM2A 2FAOA 5EXRA 2FAQA 4LIKA 4RR2A 2ATZA 1ZT2A
chains in the Genus database with same CATH topology
1V34A 4BPUA 4LIMA 1V33A 1G71A 4LILA 4MHQA 4BPXA 4BPWA 4MM2A 2FAOA 5EXRA 2FAQA 4LIKA 4RR2A 2FARA 1ZT2A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4BPU A;  4LIM A;  4LIL A;  4MHQ A;  4BPX A;  4BPW A;  4MM2 A;  2FAO A;  5EXR A;  2FAQ A;  4LIK A;  4RR2 A;  2FAR A;  1ZT2 A; 
#chains in the Genus database with same CATH topology
 1V34 A;  4BPU A;  4LIM A;  1V33 A;  1G71 A;  4LIL A;  4MHQ A;  4BPX A;  4BPW A;  2FAR A;  4MM2 A;  2FAO A;  5EXR A;  2FAQ A;  4LIK A;  4RR2 A;  2ATZ A;  1ZT2 A; 
#chains in the Genus database with same CATH homology
 1V34 A;  4BPU A;  4LIM A;  1V33 A;  1G71 A;  4LIL A;  4MHQ A;  4BPX A;  4BPW A;  4MM2 A;  2FAO A;  5EXR A;  2FAQ A;  4LIK A;  4RR2 A;  2FAR A;  1ZT2 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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#similar chains in the pdb database (?% sequence similarity)
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