2ABKA

Refinement of the native structure of endonuclease iii to a resolution of 1.85 angstrom
Total Genus 72
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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
72
sequence length
211
structure length
211
Chain Sequence
MNKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEKVDI
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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 III
publication title Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
pubmed rcsb
molecule tags Endonuclease
total genus 72
structure length 211
sequence length 211
ec nomenclature ec 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
pdb deposition date 1995-05-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00633 HHH Helix-hairpin-helix motif
A PF00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein
A PF10576 EndIII_4Fe-2S Iron-sulfur binding domain of endonuclease III
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.340.30 Mainly Alpha Orthogonal Bundle Endonuclease III; domain 1 Hypothetical protein; domain 2 2abkA01
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 2abkA02
5CHZA 4AI5A 3CWUA 3N5NX 1LWVA 1MUDA 3CVSA 1MPGA 4E9EA 1NKUA 4B24A 1PU7A 4E9HA 1VRLA 2JHNA 1KG7A 3F0ZA 1YQLA 1KG5A 1YQRA 5KN9A 4EW4A 4DK9A 2ABKA 3N0UA 1XQOA 4OFAA 4AIAA 2NOLA 5AN4A 1MUYA 1MUNA 4OFEA 2H56A 2YG9A 1N39A 4B21A 4EVVA 1M3QA 1LWWA 3CWTA 1WEGA 4UNFA 3KNTA 1PU6A 1LMZA 1KG4A 4E9FA 1PVSA 1KEAA 3CWAA 5DPKA 3IHOA 3OH6A 2NOHA 3FHFA 5KN8A 3I0XA 1XG7A 3I0WA 4EA5A 1P7MA 4B22A 1YQKA 4YPHA 4YPRA 1EBMA 4EW0A 4EJZA 2XHIA 2NOBA 4B23A 1ORPA 1FN7A 1N3CA 1WEIA 2JG6A 1PU8A 3F10A 1RRQA 2OFIA 3CVTA 1P59A 2NOIA 1KG2A 2OFKA 4PIIA 4EA4A 2YG8A 4E9GA 1RRSA 1YQMA 4UOBA 2NOEA 2I5WA 2NOZA 1LWYA 3G0QA 1KQJA 3CWSA 1ORNA 1XQPA 1KG6A 3FSPA 3D4VA 3OGDA 2JHJA 4AI4A 3IH7A 1DIZA 2NOFA 3S6IA 1NGNA 4EJYA 3FHGA 3KTUA 3CW7A 1KG3A 4YOQA 3OH9A 1M3HA 1N3AA 1HU0A 1WEFA 1KO9A 4HSBA 4OFHA
chains in the Genus database with same CATH superfamily
5CHZA 4AI5A 3OY9A 3OYEA 4ZTJA 3NNQA 3CWUA 3N5NX 1LWVA 1MUDA 3CVSA 1MPGA 4E9EA 1NKUA 4B24A 4BACA 4E7JA 1PU7A 2W04A 4E9HA 1VRLA 2JHNA 1KG7A 3F0ZA 1YQLA 1KG5A 1YQRA 3OYJA 4ZTFA 5KN9A 3OYLA 4EW4A 4DK9A 2ABKA 3N0UA 1XQOA 3OYFA 4OFAA 4AIAA 4IKFA 2NOLA 5AN4A 3L2QA 1MUYA 1MUNA 4OFEA 3L2VA 3S3OA 2H56A 2YG9A 3OYKA 3L2RA 1N39A 4B21A 4EVVA 1M3QA 1LWWA 3L2UA 3OYCA 3CWTA 3R2XC 1WEGA 3S3NA 4UNFA 3KNTA 1PU6A 1LMZA 1KG4A 4E9FA 1PVSA 1KEAA 3CWAA 3OS1A 2W03A 2V75A 5DPKA 3IHOA 2JPSA 3OH6A 4E7HA 3OYAA 3FHFA 3OYBA 2NOHA 5KN8A 3I0XA 1XG7A 3I0WA 4EA5A 1P7MA 4B22A 3L2WA 4YPHA 5FROA 4YPRA 1YQKA 1EBMA 4EW0A 4EJZA 2XHIA 2NOBA 4B23A 1ORPA 3OS2A 1FN7A 3OYGA 1N3CA 1WEIA 2JG6A 1PU8A 4E7IA 3F10A 1RRQA 2OFIA 3CVTA 3OS0A 1P59A 2NOIA 1KG2A 1U84A 2OFKA 4PIIA 4EA4A 4BDZA 2YG8A 3LCNA 4E9GA 4BDYA 1RRSA 1YQMA 4UOBA 2NOEA 2I5WA 2NOZA 1LWYA 3G0QA 1KQJA 3CWSA 1ORNA 3OYHA 3S3MA 4E7KA 1XQPA 1KG6A 3FSPA 3D4VA 4BE2A 4BE0A 4E7LA 3OGDA 2JHJA 4AI4A 3IH7A 1DIZA 2NOFA 3S6IA 1NGNA 4EJYA 3FHGA 3OYDA 3KTUA 3OYIA 3OYNA 1KG3A 3CW7A 4NZGA 4YOQA 3OH9A 1M3HA 5FRMA 1N3AA 1HU0A 3VW4A 1WEFA 3OYMA 5FRNA 1KO9A 4BE1A 4HSBA 4OFHA
chains in the Genus database with same CATH topology
5CHZA 4AI5A 3CWUA 3N5NX 1LWVA 1MUDA 3CVSA 1MPGA 4E9EA 1NKUA 4B24A 1PU7A 4E9HA 1VRLA 2JHNA 1KG7A 3F0ZA 1YQLA 1KG5A 1YQRA 5KN9A 4EW4A 4DK9A 2ABKA 3N0UA 1XQOA 4OFAA 4AIAA 2NOLA 5AN4A 1MUYA 1MUNA 4OFEA 2H56A 2YG9A 1N39A 4B21A 4EVVA 1M3QA 1LWWA 3CWTA 1WEGA 4UNFA 3KNTA 1PU6A 1LMZA 1KG4A 4E9FA 1PVSA 1KEAA 3CWAA 5DPKA 3IHOA 3OH6A 2NOHA 3FHFA 5KN8A 3I0XA 1XG7A 3I0WA 4EA5A 1P7MA 4B22A 1YQKA 4YPHA 4YPRA 1EBMA 4EW0A 4EJZA 2XHIA 2NOBA 4B23A 1ORPA 1FN7A 1N3CA 1WEIA 2JG6A 1PU8A 3F10A 1RRQA 2OFIA 3CVTA 1P59A 2NOIA 1KG2A 2OFKA 4PIIA 4EA4A 2YG8A 4E9GA 1RRSA 1YQMA 4UOBA 2NOEA 2I5WA 2NOZA 1LWYA 3G0QA 1KQJA 3CWSA 1ORNA 1XQPA 1KG6A 3FSPA 3D4VA 3OGDA 2JHJA 4AI4A 3IH7A 1DIZA 2NOFA 3S6IA 1NGNA 4EJYA 3FHGA 3KTUA 3CW7A 1KG3A 4YOQA 3OH9A 1M3HA 1N3AA 1HU0A 1WEFA 1KO9A 4HSBA 4OFHA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5CHZ A;  4AI5 A;  3CWU A;  3N5N X;  1LWV A;  1MUD A;  3CVS A;  1MPG A;  4E9E A;  1NKU A;  4B24 A;  1PU7 A;  4E9H A;  1VRL A;  2JHN A;  1KG7 A;  3F0Z A;  1YQL A;  1KG5 A;  1YQR A;  5KN9 A;  4EW4 A;  4DK9 A;  2ABK A;  3N0U A;  1XQO A;  4OFA A;  4AIA A;  2NOL A;  5AN4 A;  1MUY A;  1MUN A;  4OFE A;  2H56 A;  2YG9 A;  1N39 A;  4B21 A;  4EVV A;  1M3Q A;  1LWW A;  3CWT A;  1WEG A;  4UNF A;  3KNT A;  1PU6 A;  1LMZ A;  1KG4 A;  4E9F A;  1PVS A;  1KEA A;  3CWA A;  5DPK A;  3IHO A;  3OH6 A;  2NOH A;  3FHF A;  5KN8 A;  3I0X A;  1XG7 A;  3I0W A;  4EA5 A;  1P7M A;  4B22 A;  1YQK A;  4YPH A;  4YPR A;  1EBM A;  4EW0 A;  4EJZ A;  2XHI A;  2NOB A;  4B23 A;  1ORP A;  1FN7 A;  1N3C A;  1WEI A;  2JG6 A;  1PU8 A;  3F10 A;  1RRQ A;  2OFI A;  3CVT A;  1P59 A;  2NOI A;  1KG2 A;  2OFK A;  4PII A;  4EA4 A;  2YG8 A;  4E9G A;  1RRS A;  1YQM A;  4UOB A;  2NOE A;  2I5W A;  2NOZ A;  1LWY A;  3G0Q A;  1KQJ A;  3CWS A;  1ORN A;  1XQP A;  1KG6 A;  3FSP A;  3D4V A;  3OGD A;  2JHJ A;  4AI4 A;  3IH7 A;  1DIZ A;  2NOF A;  3S6I A;  1NGN A;  4EJY A;  3FHG A;  3KTU A;  3CW7 A;  1KG3 A;  4YOQ A;  3OH9 A;  1M3H A;  1N3A A;  1HU0 A;  1WEF A;  1KO9 A;  4HSB A;  4OFH A; 
#chains in the Genus database with same CATH topology
 5CHZ A;  4AI5 A;  3OY9 A;  3OYE A;  4ZTJ A;  3NNQ A;  3CWU A;  3N5N X;  1LWV A;  1MUD A;  3CVS A;  1MPG A;  4E9E A;  1NKU A;  4B24 A;  4BAC A;  4E7J A;  1PU7 A;  2W04 A;  4E9H A;  1VRL A;  2JHN A;  1KG7 A;  3F0Z A;  1YQL A;  1KG5 A;  1YQR A;  3OYJ A;  4ZTF A;  5KN9 A;  3OYL A;  4EW4 A;  4DK9 A;  2ABK A;  3N0U A;  1XQO A;  3OYF A;  4OFA A;  4AIA A;  4IKF A;  2NOL A;  5AN4 A;  3L2Q A;  1MUY A;  1MUN A;  4OFE A;  3L2V A;  3S3O A;  2H56 A;  2YG9 A;  3OYK A;  3L2R A;  1N39 A;  4B21 A;  4EVV A;  1M3Q A;  1LWW A;  3L2U A;  3OYC A;  3CWT A;  3R2X C;  1WEG A;  3S3N A;  4UNF A;  3KNT A;  1PU6 A;  1LMZ A;  1KG4 A;  4E9F A;  1PVS A;  1KEA A;  3CWA A;  3OS1 A;  2W03 A;  2V75 A;  5DPK A;  3IHO A;  2JPS A;  3OH6 A;  4E7H A;  3OYA A;  3FHF A;  3OYB A;  2NOH A;  5KN8 A;  3I0X A;  1XG7 A;  3I0W A;  4EA5 A;  1P7M A;  4B22 A;  3L2W A;  4YPH A;  5FRO A;  4YPR A;  1YQK A;  1EBM A;  4EW0 A;  4EJZ A;  2XHI A;  2NOB A;  4B23 A;  1ORP A;  3OS2 A;  1FN7 A;  3OYG A;  1N3C A;  1WEI A;  2JG6 A;  1PU8 A;  4E7I A;  3F10 A;  1RRQ A;  2OFI A;  3CVT A;  3OS0 A;  1P59 A;  2NOI A;  1KG2 A;  1U84 A;  2OFK A;  4PII A;  4EA4 A;  4BDZ A;  2YG8 A;  3LCN A;  4E9G A;  4BDY A;  1RRS A;  1YQM A;  4UOB A;  2NOE A;  2I5W A;  2NOZ A;  1LWY A;  3G0Q A;  1KQJ A;  3CWS A;  1ORN A;  3OYH A;  3S3M A;  4E7K A;  1XQP A;  1KG6 A;  3FSP A;  3D4V A;  4BE2 A;  4BE0 A;  4E7L A;  3OGD A;  2JHJ A;  4AI4 A;  3IH7 A;  1DIZ A;  2NOF A;  3S6I A;  1NGN A;  4EJY A;  3FHG A;  3OYD A;  3KTU A;  3OYI A;  3OYN A;  1KG3 A;  3CW7 A;  4NZG A;  4YOQ A;  3OH9 A;  1M3H A;  5FRM A;  1N3A A;  1HU0 A;  3VW4 A;  1WEF A;  3OYM A;  5FRN A;  1KO9 A;  4BE1 A;  4HSB A;  4OFH A; 
#chains in the Genus database with same CATH homology
 5CHZ A;  4AI5 A;  3CWU A;  3N5N X;  1LWV A;  1MUD A;  3CVS A;  1MPG A;  4E9E A;  1NKU A;  4B24 A;  1PU7 A;  4E9H A;  1VRL A;  2JHN A;  1KG7 A;  3F0Z A;  1YQL A;  1KG5 A;  1YQR A;  5KN9 A;  4EW4 A;  4DK9 A;  2ABK A;  3N0U A;  1XQO A;  4OFA A;  4AIA A;  2NOL A;  5AN4 A;  1MUY A;  1MUN A;  4OFE A;  2H56 A;  2YG9 A;  1N39 A;  4B21 A;  4EVV A;  1M3Q A;  1LWW A;  3CWT A;  1WEG A;  4UNF A;  3KNT A;  1PU6 A;  1LMZ A;  1KG4 A;  4E9F A;  1PVS A;  1KEA A;  3CWA A;  5DPK A;  3IHO A;  3OH6 A;  2NOH A;  3FHF A;  5KN8 A;  3I0X A;  1XG7 A;  3I0W A;  4EA5 A;  1P7M A;  4B22 A;  1YQK A;  4YPH A;  4YPR A;  1EBM A;  4EW0 A;  4EJZ A;  2XHI A;  2NOB A;  4B23 A;  1ORP A;  1FN7 A;  1N3C A;  1WEI A;  2JG6 A;  1PU8 A;  3F10 A;  1RRQ A;  2OFI A;  3CVT A;  1P59 A;  2NOI A;  1KG2 A;  2OFK A;  4PII A;  4EA4 A;  2YG8 A;  4E9G A;  1RRS A;  1YQM A;  4UOB A;  2NOE A;  2I5W A;  2NOZ A;  1LWY A;  3G0Q A;  1KQJ A;  3CWS A;  1ORN A;  1XQP A;  1KG6 A;  3FSP A;  3D4V A;  3OGD A;  2JHJ A;  4AI4 A;  3IH7 A;  1DIZ A;  2NOF A;  3S6I A;  1NGN A;  4EJY A;  3FHG A;  3KTU A;  3CW7 A;  1KG3 A;  4YOQ A;  3OH9 A;  1M3H A;  1N3A A;  1HU0 A;  1WEF A;  1KO9 A;  4HSB A;  4OFH 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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