1ORPA

Structure of a trapped endonuclease iii-dna covalent intermediate: estranged-adenine complex
Total Genus 75
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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
75
sequence length
213
structure length
213
Chain Sequence
MLTKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKKRMR
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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 5'-D(*AP*AP*GP*AP*CP*AP*TP*GP*GP*AP*C)-3'
publication title Structure of a Trapped Endonuclease III-DNA Covalent Intermediate
pubmed doi rcsb
source organism Geobacillus stearothermophilus
molecule tags Hydrolase/dna
total genus 75
structure length 213
sequence length 213
ec nomenclature
pdb deposition date 2003-03-14
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 1orpA01
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 1orpA02
1YQKA 1NGNA 2NOFA 1MUDA 1KG7A 1KG4A 2NOIA 1LWVA 2NOZA 4OFAA 1MUYA 1LWYA 1WEFA 1KG5A 1M3HA 1N3CA 3CWTA 4YPRA 4OFHA 1XG7A 4YOQA 4B22A 4EA4A 1YQLA 1PU7A 4B24A 4PIIA 1P59A 3S6IA 1KQJA 1LMZA 3F10A 3FSPA 4DK9A 1FN7A 3N5NX 3F0ZA 4AI5A 4E9HA 3IHOA 1DIZA 3KTUA 1P7MA 1KG6A 1YQMA 1ORNA 5DPKA 5KN8A 4HSBA 3IH7A 2H56A 4EVVA 2YG8A 4EW0A 4B21A 3OH6A 1RRQA 3D4VA 3OH9A 3CWUA 1M3QA 5AN4A 1HU0A 1WEGA 2YG9A 4EJZA 4OFEA 2NOHA 2XHIA 3KNTA 4AIAA 5CHZA 4EJYA 4B23A 2OFKA 1MPGA 1WEIA 4E9EA 3FHFA 2OFIA 2NOEA 3I0WA 4E9GA 1KEAA 1N3AA 2JHNA 2NOBA 4AI4A 4YPHA 3G0QA 1RRSA 4E9FA 1N39A 1PU6A 1KG3A 4EA5A 1KG2A 1PU8A 5KN9A 1EBMA 4UOBA 4UNFA 2ABKA 3CVTA 3FHGA 1KO9A 2JG6A 1VRLA 1YQRA 3CVSA 1NKUA 2I5WA 3OGDA 1MUNA 4EW4A 3CWSA 1PVSA 1LWWA 3CW7A 1XQPA 3I0XA 1ORPA 3CWAA 2NOLA 3N0UA 1XQOA 2JHJA
chains in the Genus database with same CATH superfamily
4BACA 1YQKA 1NGNA 2NOFA 3OYKA 3OYBA 1MUDA 1KG7A 3OY9A 1KG4A 2NOIA 1LWVA 3OYNA 2NOZA 4OFAA 1MUYA 1LWYA 4E7IA 1WEFA 1KG5A 3OS0A 1M3HA 1N3CA 3CWTA 4YPRA 4OFHA 1XG7A 4YOQA 4B22A 4EA4A 1YQLA 1PU7A 4B24A 4E7KA 4PIIA 1P59A 3S6IA 1KQJA 5FRMA 1LMZA 3L2VA 3F10A 3FSPA 3OYCA 4DK9A 3L2RA 1FN7A 3OYHA 3N5NX 3F0ZA 4AI5A 4E9HA 3IHOA 3OS2A 1DIZA 3KTUA 4E7HA 1P7MA 1KG6A 5FROA 4BDZA 1YQMA 1ORNA 4BDYA 5DPKA 5KN8A 4HSBA 3IH7A 2H56A 4EVVA 2YG8A 4EW0A 3NNQA 4B21A 3OH6A 1RRQA 3D4VA 3OH9A 3CWUA 1M3QA 5AN4A 3LCNA 1WEGA 3L2WA 4E7LA 1HU0A 2JPSA 2YG9A 3L2QA 3S3MA 4EJZA 4OFEA 3OYLA 2NOHA 2XHIA 4BE1A 3KNTA 4AIAA 4ZTFA 3OYAA 5CHZA 4EJYA 3VW4A 3OYGA 4B23A 2OFKA 1MPGA 1WEIA 4E9EA 3FHFA 3OYDA 4BE2A 3OYFA 4IKFA 2OFIA 2V75A 2NOEA 3S3OA 3I0WA 4E9GA 4ZTJA 1KEAA 4BE0A 1N3AA 2JHNA 2NOBA 4AI4A 4YPHA 3G0QA 1RRSA 2W03A 4E9FA 1N39A 1PU6A 3OYMA 1KG3A 3R2XC 4EA5A 3L2UA 1KG2A 4E7JA 1PU8A 5KN9A 1EBMA 4UOBA 3S3NA 4UNFA 2ABKA 3OS1A 3CVTA 1U84A 2W04A 1KO9A 3FHGA 3OYEA 2JG6A 1VRLA 1YQRA 3CVSA 3OYJA 1NKUA 5FRNA 3OYIA 3OGDA 2I5WA 1MUNA 4EW4A 3CWSA 1PVSA 1LWWA 3CW7A 1XQPA 3I0XA 1ORPA 3CWAA 2NOLA 3N0UA 4NZGA 1XQOA 2JHJA
chains in the Genus database with same CATH topology
1YQKA 1NGNA 2NOFA 1MUDA 1KG7A 1KG4A 2NOIA 1LWVA 2NOZA 4OFAA 1MUYA 1LWYA 1WEFA 1KG5A 1M3HA 1N3CA 3CWTA 4YPRA 4OFHA 1XG7A 4YOQA 4B22A 4EA4A 1YQLA 1PU7A 4B24A 4PIIA 1P59A 3S6IA 1KQJA 1LMZA 3F10A 3FSPA 4DK9A 1FN7A 3N5NX 3F0ZA 4AI5A 4E9HA 3IHOA 1DIZA 3KTUA 1P7MA 1KG6A 1YQMA 1ORNA 5DPKA 5KN8A 4HSBA 3IH7A 2H56A 4EVVA 2YG8A 4EW0A 4B21A 3OH6A 1RRQA 3D4VA 3OH9A 3CWUA 1M3QA 5AN4A 1HU0A 1WEGA 2YG9A 4EJZA 4OFEA 2NOHA 2XHIA 3KNTA 4AIAA 5CHZA 4EJYA 4B23A 2OFKA 1MPGA 1WEIA 4E9EA 3FHFA 2OFIA 2NOEA 3I0WA 4E9GA 1KEAA 1N3AA 2JHNA 2NOBA 4AI4A 4YPHA 3G0QA 1RRSA 4E9FA 1N39A 1PU6A 1KG3A 4EA5A 1KG2A 1PU8A 5KN9A 1EBMA 4UOBA 4UNFA 2ABKA 3CVTA 3FHGA 1KO9A 2JG6A 1VRLA 1YQRA 3CVSA 1NKUA 2I5WA 3OGDA 1MUNA 4EW4A 3CWSA 1PVSA 1LWWA 3CW7A 1XQPA 3I0XA 1ORPA 3CWAA 2NOLA 3N0UA 1XQOA 2JHJA
chains in the Genus database with same CATH homology


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