5GKPA

Crystal structure of the endog worm homologue cps-6 h148a/f122a in complex with dna
Total Genus 64
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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
64
sequence length
238
structure length
235
Chain Sequence
SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKGVDRKLCEAKPDITFPQKFLSQNTDYKCSGFDRGALAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGA
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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.

Chord Diagram
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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
molecule tags Hydrolase/dna
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
1QAEA 5INHA 3WAXA 4A1NA 4GTXA 4GTZA 1QL0A 5KXAA 5LQQA 1SMNA 3WAVA 4ZG6A 3NKOA 4ZG7A 2O3BA 1G8TA 5L0EA 5GKCA 4ZG9A 3ISMA 5DLWA 4GTWA 4ZGAA 5DLTA 2XR9A 5GKPA 3OWVA 5L0BA 5IJQA 5HRTA 3NKPA 4QGOA 4QN0A 3NKRA 3WAYA 5IJSA 5LIAA 1ZM8A 4E3YA 2XH3A 4QH0A 3S5BA 3NKMA 3NKNA 2XRGA 3WAWA 5L0KA 4B56A 3NKQA 2XGRA 5DLVA 4GTYA
chains in the Genus database with same CATH superfamily
1QAEA 5INHA 3WAXA 4A1NA 4GTXA 4GTZA 1QL0A 5KXAA 5LQQA 1SMNA 3WAVA 4ZG6A 3NKOA 4ZG7A 2O3BA 1G8TA 5L0EA 5GKCA 4ZG9A 3ISMA 5DLWA 4GTWA 4ZGAA 5DLTA 2XR9A 5GKPA 3OWVA 5L0BA 5IJQA 5HRTA 3NKPA 4QGOA 4QN0A 3NKRA 3WAYA 5IJSA 5LIAA 1ZM8A 4E3YA 2XH3A 4QH0A 3S5BA 3NKMA 3NKNA 2XRGA 3WAWA 5L0KA 4B56A 3NKQA 2XGRA 5DLVA 4GTYA
chains in the Genus database with same CATH topology
1QAEA 5INHA 3WAXA 4A1NA 4GTXA 4GTZA 1QL0A 5KXAA 5LQQA 1SMNA 3WAVA 4ZG6A 3NKOA 4ZG7A 2O3BA 1G8TA 5L0EA 5GKCA 4ZG9A 3ISMA 5DLWA 4GTWA 4ZGAA 5DLTA 2XR9A 5GKPA 3OWVA 5L0BA 5IJQA 5HRTA 3NKPA 4QGOA 4QN0A 3NKRA 3WAYA 5IJSA 5LIAA 1ZM8A 4E3YA 2XH3A 4QH0A 3S5BA 3NKMA 3NKNA 2XRGA 3WAWA 5L0KA 4B56A 3NKQA 2XGRA 5DLVA 4GTYA
chains in the Genus database with same CATH homology


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