2YG8A

Structure of an unusual 3-methyladenine dna glycosylase ii (alka) from deinococcus radiodurans
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
207
structure length
207
Chain Sequence
LPAVLPPLTDHAGAVAHLSRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGEDWRDVTARWAPYRSLASRYLWANSARMQAGGAPL
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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 Hydrolase
molecule keywords DNA-3-methyladenine glycosidase II, putative
publication title Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.
pubmed doi rcsb
source organism Deinococcus radiodurans
total genus 64
structure length 207
sequence length 207
chains with identical sequence B
ec nomenclature
pdb deposition date 2011-04-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein
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 2yg8A02
1.10.1670.40 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Endonuclease Iii, domain 2 2yg8A01
4B22A 1KQJA 3G0QA 3N5NX 2JG6A 3OH9A 4E9FA 1YQKA 4B24A 1N3CA 1N3AA 4OFAA 1LWYA 1NKUA 4E9HA 1M3QA 1HU0A 4YPRA 4AI4A 3KTUA 1PU7A 1YQMA 1EBMA 2YG8A 1KEAA 3I0WA 5DPKA 3CWTA 2NOEA 2XHIA 4EJYA 4YOQA 4EVVA 4EA5A 3FHFA 1KG4A 2H56A 4OFEA 4DK9A 3S6IA 1P59A 1LWWA 5KN8A 3I0XA 5KN9A 1DIZA 1XQOA 1KG2A 3IH7A 4B23A 2I5WA 2YG9A 3CW7A 1MUNA 4YPHA 1LMZA 2OFIA 1FN7A 1ORNA 3CVTA 3CWUA 3IHOA 2OFKA 3CWAA 1ORPA 4UOBA 2ABKA 2JHNA 1PU8A 1WEIA 1MUDA 1PVSA 2NOZA 1XQPA 2NOIA 1MPGA 1PU6A 3FSPA 3FHGA 2NOBA 1MUYA 2JHJA 3F0ZA 1RRQA 1M3HA 1YQRA 4PIIA 1KG3A 1N39A 1KO9A 1RRSA 4OFHA 3N0UA 5CHZA 2NOFA 1VRLA 3D4VA 2NOLA 1KG7A 1KG5A 1KG6A 4EA4A 3OH6A 3CVSA 3F10A 4EJZA 4E9EA 1WEFA 3OGDA 4AIAA 4EW0A 2NOHA 5AN4A 1LWVA 4E9GA 4AI5A 3KNTA 4HSBA 1NGNA 1P7MA 4UNFA 4EW4A 1XG7A 4B21A 3CWSA 1YQLA 1WEGA
chains in the Genus database with same CATH superfamily
4B22A 1KQJA 3G0QA 3N5NX 2JG6A 3OYLA 3OH9A 4E9FA 1YQKA 3LCNA 3OS1A 1U84A 4B24A 1N3CA 1N3AA 2W04A 4OFAA 3OYFA 3OYBA 4BE0A 1NKUA 4ZTFA 1LWYA 3L2RA 4E9HA 1M3QA 1HU0A 4YPRA 4AI4A 3OYNA 3KTUA 2W03A 1PU7A 1YQMA 1EBMA 2YG8A 1KEAA 2JPSA 3I0WA 5DPKA 3CWTA 2NOEA 2XHIA 4EJYA 4YOQA 4EVVA 4EA5A 3FHFA 1KG4A 2H56A 4NZGA 4OFEA 4DK9A 3S6IA 4BDYA 1P59A 1LWWA 5KN8A 3I0XA 3S3MA 5KN9A 1DIZA 1XQOA 1KG2A 3IH7A 3R2XC 4E7LA 4B23A 3OYMA 4BE1A 2I5WA 2YG9A 3CW7A 1MUNA 4YPHA 1LMZA 3OYCA 3OYIA 4E7JA 2OFIA 3OYEA 1FN7A 1ORNA 3CVTA 3CWUA 3IHOA 2OFKA 3CWAA 1ORPA 3L2QA 4UOBA 4BE2A 2ABKA 3OYAA 2JHNA 1PU8A 3L2WA 3VW4A 1WEIA 1MUDA 1PVSA 2NOZA 4BACA 1XQPA 2NOIA 1MPGA 3OYJA 1PU6A 3FSPA 3FHGA 2NOBA 1MUYA 2JHJA 3F0ZA 1RRQA 4IKFA 1M3HA 1YQRA 3OYKA 4PIIA 1KG3A 1N39A 1KO9A 3NNQA 3L2VA 1RRSA 4OFHA 3OYGA 3N0UA 5CHZA 3OYHA 2NOFA 1VRLA 4BDZA 3D4VA 2NOLA 1KG7A 5FROA 3L2UA 1KG5A 1KG6A 3OYDA 4EA4A 3OH6A 4E7IA 3CVSA 3F10A 5FRMA 4EJZA 3S3OA 4E9EA 4E7KA 1WEFA 3OS0A 3OGDA 4AIAA 4EW0A 2NOHA 5FRNA 5AN4A 3OS2A 1LWVA 4E9GA 4E7HA 4AI5A 3KNTA 3S3NA 4HSBA 1NGNA 1P7MA 4UNFA 4EW4A 4ZTJA 1XG7A 4B21A 3CWSA 1YQLA 3OY9A 1WEGA 2V75A
chains in the Genus database with same CATH topology
4B22A 1KQJA 3G0QA 3N5NX 2JG6A 3OH9A 4E9FA 1YQKA 4B24A 1N3CA 1N3AA 4OFAA 1LWYA 1NKUA 4E9HA 1M3QA 1HU0A 4YPRA 4AI4A 3KTUA 1PU7A 1YQMA 1EBMA 2YG8A 1KEAA 3I0WA 5DPKA 3CWTA 2NOEA 2XHIA 4EJYA 4YOQA 4EVVA 4EA5A 3FHFA 1KG4A 2H56A 4OFEA 4DK9A 3S6IA 1P59A 1LWWA 5KN8A 3I0XA 5KN9A 1DIZA 1XQOA 1KG2A 3IH7A 4B23A 2I5WA 2YG9A 3CW7A 1MUNA 4YPHA 1LMZA 2OFIA 1FN7A 1ORNA 3CVTA 3CWUA 3IHOA 2OFKA 3CWAA 1ORPA 4UOBA 2ABKA 2JHNA 1PU8A 1WEIA 1MUDA 1PVSA 2NOZA 1XQPA 2NOIA 1MPGA 1PU6A 3FSPA 3FHGA 2NOBA 1MUYA 2JHJA 3F0ZA 1RRQA 1M3HA 1YQRA 4PIIA 1KG3A 1N39A 1KO9A 1RRSA 4OFHA 3N0UA 5CHZA 2NOFA 1VRLA 3D4VA 2NOLA 1KG7A 1KG5A 1KG6A 4EA4A 3OH6A 3CVSA 3F10A 4EJZA 4E9EA 1WEFA 3OGDA 4AIAA 4EW0A 2NOHA 5AN4A 1LWVA 4E9GA 4AI5A 3KNTA 4HSBA 1NGNA 1P7MA 4UNFA 4EW4A 1XG7A 4B21A 3CWSA 1YQLA 1WEGA
chains in the Genus database with same CATH homology


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