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 tags Endonuclease
molecule keywords ENDONUCLEASE III
publication title Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
pubmed rcsb
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
2YG9A 4E9GA 1NGNA 1MUDA 4PIIA 4E9FA 4OFAA 2JHNA 4EW0A 1WEIA 1DIZA 5CHZA 1KQJA 1WEFA 1NKUA 1P59A 1WEGA 4B24A 1KG4A 1P7MA 1YQLA 5AN4A 1MUNA 5DPKA 1N3AA 3CWTA 4AI5A 4HSBA 1KG3A 1LWWA 2OFIA 4EJYA 1ORNA 1VRLA 4YOQA 1YQRA 1ORPA 2JG6A 1XG7A 1PU8A 1N39A 4EW4A 1LMZA 3D4VA 1KG7A 4B22A 3CW7A 3S6IA 1HU0A 3OH6A 3FSPA 3CWUA 4OFHA 4B23A 2NOIA 4AI4A 4EA5A 4UNFA 3OGDA 3I0WA 2XHIA 1RRQA 4EVVA 1M3QA 3KNTA 1XQOA 1FN7A 1XQPA 1KEAA 3G0QA 4B21A 3CWSA 2NOZA 4E9EA 3F0ZA 3N5NX 1LWVA 4UOBA 1YQMA 2OFKA 1KG2A 4YPRA 1YQKA 2H56A 4DK9A 1KG5A 1KO9A 3IHOA 3CWAA 4E9HA 5KN9A 2NOHA 1RRSA 4EJZA 3OH9A 3KTUA 1KG6A 3N0UA 3I0XA 1M3HA 2YG8A 1N3CA 3F10A 2NOLA 3CVTA 4OFEA 1PVSA 3FHFA 4AIAA 4YPHA 1PU6A 2JHJA 2ABKA 1LWYA 1EBMA 5KN8A 2I5WA 3CVSA 1MPGA 2NOBA 3FHGA 1MUYA 3IH7A 2NOEA 2NOFA 1PU7A 4EA4A
chains in the Genus database with same CATH superfamily
2YG9A 4E9GA 1NGNA 1MUDA 3OYJA 4BACA 4PIIA 2JPSA 4E7LA 4E9FA 4OFAA 4BE0A 2JHNA 3OYLA 4EW0A 1WEIA 3OYDA 1DIZA 5CHZA 1KQJA 2V75A 3OS1A 1WEFA 1NKUA 5FRMA 4IKFA 1P59A 1WEGA 3OYHA 4B24A 1KG4A 1P7MA 1YQLA 3OYMA 5AN4A 1MUNA 3OS2A 5DPKA 3S3NA 1N3AA 4AI5A 3CWTA 4E7HA 4HSBA 1KG3A 1LWWA 2OFIA 4EJYA 3OYAA 1ORNA 2W04A 1VRLA 4YOQA 1YQRA 1ORPA 2JG6A 1XG7A 1PU8A 1N39A 4EW4A 3OYNA 1LMZA 3D4VA 1KG7A 1U84A 3S3MA 4B22A 3CW7A 3S6IA 2W03A 1HU0A 4BE2A 3OH6A 3FSPA 3CWUA 3L2WA 4OFHA 3LCNA 4B23A 3VW4A 2NOIA 3L2RA 3OYKA 5FROA 4AI4A 3OYGA 4EA5A 4UNFA 3OGDA 4BE1A 3I0WA 3NNQA 2XHIA 1RRQA 4ZTJA 4EVVA 1M3QA 3OYIA 3KNTA 1XQOA 1FN7A 1XQPA 3OYCA 1KEAA 3G0QA 4B21A 3OYFA 3CWSA 4ZTFA 4E9EA 3F0ZA 2NOZA 3N5NX 1LWVA 4UOBA 1YQMA 2OFKA 5FRNA 4E7JA 1KG2A 4YPRA 4E7IA 1YQKA 3R2XC 2H56A 4DK9A 1KG5A 1KO9A 3IHOA 3CWAA 4E9HA 5KN9A 2NOHA 4E7KA 1RRSA 4EJZA 3OH9A 3OS0A 3KTUA 1KG6A 3N0UA 3I0XA 1M3HA 3L2VA 2YG8A 3S3OA 3F10A 1N3CA 2NOLA 3CVTA 4OFEA 1PVSA 4BDYA 3FHFA 4AIAA 4YPHA 3OYEA 3OY9A 1PU6A 2JHJA 2ABKA 4BDZA 1LWYA 3L2QA 4NZGA 1EBMA 5KN8A 2I5WA 3CVSA 1MPGA 3L2UA 3OYBA 2NOBA 3FHGA 1MUYA 3IH7A 2NOEA 2NOFA 1PU7A 4EA4A
chains in the Genus database with same CATH topology
2YG9A 4E9GA 1NGNA 1MUDA 4PIIA 4E9FA 4OFAA 2JHNA 4EW0A 1WEIA 1DIZA 5CHZA 1KQJA 1WEFA 1NKUA 1P59A 1WEGA 4B24A 1KG4A 1P7MA 1YQLA 5AN4A 1MUNA 5DPKA 1N3AA 3CWTA 4AI5A 4HSBA 1KG3A 1LWWA 2OFIA 4EJYA 1ORNA 1VRLA 4YOQA 1YQRA 1ORPA 2JG6A 1XG7A 1PU8A 1N39A 4EW4A 1LMZA 3D4VA 1KG7A 4B22A 3CW7A 3S6IA 1HU0A 3OH6A 3FSPA 3CWUA 4OFHA 4B23A 2NOIA 4AI4A 4EA5A 4UNFA 3OGDA 3I0WA 2XHIA 1RRQA 4EVVA 1M3QA 3KNTA 1XQOA 1FN7A 1XQPA 1KEAA 3G0QA 4B21A 3CWSA 2NOZA 4E9EA 3F0ZA 3N5NX 1LWVA 4UOBA 1YQMA 2OFKA 1KG2A 4YPRA 1YQKA 2H56A 4DK9A 1KG5A 1KO9A 3IHOA 3CWAA 4E9HA 5KN9A 2NOHA 1RRSA 4EJZA 3OH9A 3KTUA 1KG6A 3N0UA 3I0XA 1M3HA 2YG8A 1N3CA 3F10A 2NOLA 3CVTA 4OFEA 1PVSA 3FHFA 4AIAA 4YPHA 1PU6A 2JHJA 2ABKA 1LWYA 1EBMA 5KN8A 2I5WA 3CVSA 1MPGA 2NOBA 3FHGA 1MUYA 3IH7A 2NOEA 2NOFA 1PU7A 4EA4A
chains in the Genus database with same CATH homology


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