5GKPA

Crystal structure of the endog worm homologue cps-6 h148a/f122a in complex with dna
Total Genus 64
Loading diagram...

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
64
sequence length
238
structure length
235
Chain Sequence
SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKGVDRKLCEAKPDITFPQKFLSQNTDYKCSGFDRGALAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGA
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
molecule tags Hydrolase/dna
molecule keywords Endonuclease G, mitochondrial
publication title Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.
pubmed doi rcsb
source organism Caenorhabditis elegans
total genus 64
structure length 235
sequence length 238
chains with identical sequence B
ec nomenclature ec 3.1.30.-:
pdb deposition date 2016-07-05

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01223 Endonuclease_NS DNA/RNA non-specific endonuclease
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.570.10 Alpha Beta 3-Layer(aba) Sandwich Extracellular Endonuclease; Chain A Extracellular Endonuclease, subunit A 5gkpA00
1QL0A 1G8TA 3WAVA 4ZG7A 3WAYA 2O3BA 3NKPA 5GKCA 5KXAA 2XR9A 5HRTA 1SMNA 4GTZA 4B56A 4ZGAA 5GKPA 4QGOA 2XRGA 4ZG6A 5DLVA 3OWVA 5IJSA 4ZG9A 3ISMA 5DLWA 3NKNA 3S5BA 4QH0A 2XGRA 3NKMA 3NKOA 5IJQA 5L0BA 5LQQA 1ZM8A 4E3YA 4QN0A 3NKQA 4GTWA 5L0EA 2XH3A 5DLTA 4A1NA 4GTYA 4GTXA 5L0KA 3WAXA 1QAEA 5INHA 5LIAA 3WAWA 3NKRA
chains in the Genus database with same CATH superfamily
1QL0A 1G8TA 3WAVA 4ZG7A 3WAYA 2O3BA 3NKPA 5GKCA 5KXAA 2XR9A 5HRTA 1SMNA 4GTZA 4B56A 4ZGAA 5GKPA 4QGOA 2XRGA 4ZG6A 5DLVA 3OWVA 5IJSA 4ZG9A 3ISMA 5DLWA 3NKNA 3S5BA 4QH0A 2XGRA 3NKMA 3NKOA 5IJQA 5L0BA 5LQQA 1ZM8A 4E3YA 4QN0A 3NKQA 4GTWA 5L0EA 2XH3A 5DLTA 4A1NA 4GTYA 4GTXA 5L0KA 3WAXA 1QAEA 5INHA 5LIAA 3WAWA 3NKRA
chains in the Genus database with same CATH topology
1QL0A 1G8TA 3WAVA 4ZG7A 3WAYA 2O3BA 3NKPA 5GKCA 5KXAA 2XR9A 5HRTA 1SMNA 4GTZA 4B56A 4ZGAA 5GKPA 4QGOA 2XRGA 4ZG6A 5DLVA 3OWVA 5IJSA 4ZG9A 3ISMA 5DLWA 3NKNA 3S5BA 4QH0A 2XGRA 3NKMA 3NKOA 5IJQA 5L0BA 5LQQA 1ZM8A 4E3YA 4QN0A 3NKQA 4GTWA 5L0EA 2XH3A 5DLTA 4A1NA 4GTYA 4GTXA 5L0KA 3WAXA 1QAEA 5INHA 5LIAA 3WAWA 3NKRA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1QL0 A;  1G8T A;  3WAV A;  4ZG7 A;  3WAY A;  2O3B A;  3NKP A;  5GKC A;  5KXA A;  2XR9 A;  5HRT A;  1SMN A;  4GTZ A;  4B56 A;  4ZGA A;  5GKP A;  4QGO A;  2XRG A;  4ZG6 A;  5DLV A;  3OWV A;  5IJS A;  4ZG9 A;  3ISM A;  5DLW A;  3NKN A;  3S5B A;  4QH0 A;  2XGR A;  3NKM A;  3NKO A;  5IJQ A;  5L0B A;  5LQQ A;  1ZM8 A;  4E3Y A;  4QN0 A;  3NKQ A;  4GTW A;  5L0E A;  2XH3 A;  5DLT A;  4A1N A;  4GTY A;  4GTX A;  5L0K A;  3WAX A;  1QAE A;  5INH A;  5LIA A;  3WAW A;  3NKR A; 
#chains in the Genus database with same CATH topology
 1QL0 A;  1G8T A;  3WAV A;  4ZG7 A;  3WAY A;  2O3B A;  3NKP A;  5GKC A;  5KXA A;  2XR9 A;  5HRT A;  1SMN A;  4GTZ A;  4B56 A;  4ZGA A;  5GKP A;  4QGO A;  2XRG A;  4ZG6 A;  5DLV A;  3OWV A;  5IJS A;  4ZG9 A;  3ISM A;  5DLW A;  3NKN A;  3S5B A;  4QH0 A;  2XGR A;  3NKM A;  3NKO A;  5IJQ A;  5L0B A;  5LQQ A;  1ZM8 A;  4E3Y A;  4QN0 A;  3NKQ A;  4GTW A;  5L0E A;  2XH3 A;  5DLT A;  4A1N A;  4GTY A;  4GTX A;  5L0K A;  3WAX A;  1QAE A;  5INH A;  5LIA A;  3WAW A;  3NKR A; 
#chains in the Genus database with same CATH homology
 1QL0 A;  1G8T A;  3WAV A;  4ZG7 A;  3WAY A;  2O3B A;  3NKP A;  5GKC A;  5KXA A;  2XR9 A;  5HRT A;  1SMN A;  4GTZ A;  4B56 A;  4ZGA A;  5GKP A;  4QGO A;  2XRG A;  4ZG6 A;  5DLV A;  3OWV A;  5IJS A;  4ZG9 A;  3ISM A;  5DLW A;  3NKN A;  3S5B A;  4QH0 A;  2XGR A;  3NKM A;  3NKO A;  5IJQ A;  5L0B A;  5LQQ A;  1ZM8 A;  4E3Y A;  4QN0 A;  3NKQ A;  4GTW A;  5L0E A;  2XH3 A;  5DLT A;  4A1N A;  4GTY A;  4GTX A;  5L0K A;  3WAX A;  1QAE A;  5INH A;  5LIA A;  3WAW A;  3NKR A; 
...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...