5GKC | Genus

Total Genus 70

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	70
sequence length	242
structure length	238
Chain Sequence	GSPSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKVDRKLCEAKPDITFPQKFLSQNTDYKCSGFDRGALAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK

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

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The Resolver thinks Pdb

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reading 238 atoms

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238 atoms created

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Hydrolase
source organism	Caenorhabditis elegans
publication title	Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. pubmed doi rcsb
molecule keywords	Endonuclease G, mitochondrial
total genus	70
structure length	238
sequence length	242
chains with identical sequence	B
ec nomenclature	ec 3.1.30.-:
pdb deposition date	2016-07-04

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	Class	Architecture	Topology	Homology	Domain
3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease; Chain A	Extracellular Endonuclease, subunit A	5gkcA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations