3OGDA

Alka undamaged dna complex: interrogation of a g*:c base pair
Total Genus 87
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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
87
sequence length
288
structure length
288
Chain Sequence
MADIGSEFYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQCVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDE
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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 DNA-3-methyladenine glycosylase 2
publication title Structure of Escherichia coli AlkA in Complex with Undamaged DNA.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Hydrolase/dna
total genus 87
structure length 288
sequence length 288
ec nomenclature ec 3.2.2.21: DNA-3-methyladenine glycosylase II.
pdb deposition date 2010-08-16

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 3ogdA02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3ogdA03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3ogdA01
2OFKA 4OFAA 1KG2A 3S6IA 1PU8A 4AI5A 4AIAA 1RRQA 4DK9A 3CVTA 2NOBA 3KNTA 1P7MA 4EVVA 1MPGA 1MUNA 3FHFA 4YOQA 4EW4A 3I0XA 1P59A 1KG3A 2NOZA 5CHZA 1KG5A 4OFEA 4EA5A 1YQMA 1PVSA 1ORNA 2H56A 5DPKA 3IH7A 5KN8A 4YPRA 1M3QA 1PU6A 3FHGA 4EJYA 2YG8A 2ABKA 1RRSA 2OFIA 1PU7A 1KG7A 3CWSA 3I0WA 1WEFA 3FSPA 1KEAA 1WEIA 3CVSA 1XQOA 2NOIA 1NKUA 3KTUA 1EBMA 3CWAA 4AI4A 4UOBA 1KQJA 1ORPA 1NGNA 1XQPA 3IHOA 3CWUA 1KO9A 1YQKA 2XHIA 5AN4A 4OFHA 1HU0A 1M3HA 3D4VA 1VRLA 4E9GA 3OH9A 4E9FA 2NOLA 1LWYA 4B22A 2JHNA 4B23A 1LWVA 4B21A 3N0UA 2JG6A 2YG9A 1DIZA 4UNFA 2JHJA 1MUDA 2NOFA 4PIIA 1KG6A 1N3AA 1YQRA 1LWWA 1YQLA 2NOHA 3OH6A 3N5NX 1KG4A 1LMZA 1MUYA 4E9HA 1WEGA 4B24A 3G0QA 3F0ZA 1N3CA 3F10A 4EJZA 4HSBA 3OGDA 3CW7A 4YPHA 3CWTA 4EW0A 5KN9A 4E9EA 1FN7A 2NOEA 1XG7A 1N39A 4EA4A 2I5WA
chains in the Genus database with same CATH superfamily
4ROEB 1W80A 5FRMA 1PCMX 3OSEA 3S6IA 1QN7A 4RODB 4DK9A 2DKAA 3KNTA 3OS2A 1TGHA 1B9KA 1WJWA 1P59A 1KG3A 4TPSA 1CDWA 4WX8A 1ORNA 2H56A 1QNEA 3H1ZA 3HS9A 5HSHA 3OYNA 1C47A 1J3MA 3OCIA 5JN5A 5IYDP 1RRSA 1PCJX 3OLPA 4E7LA 1PU7A 1KG7A 1WEFA 4IL8A 3ASMA 1WEIA 2VJ0A 2JPSA 3EAYA 2NOIA 1QN4A 4QG5A 3KTUA 1EBMA 1M5Q1 3CWAA 4E7KA 5FRNA 3ENCA 3CWUA 2ZFDB 1K35A 1M3HA 1K2YX 3L2RA 3DPTA 4E7JA 3VW4A 1C4GA 2HZSA 3OYEA 1KFIA 1WQAA 3TDHA 2D0AA 2IV9A 4MRQA 4B21A 3UW2A 4BE1A 1QN9A 3N89A 1V5SA 2FUVA 2V92A 1QN8A 3S3MA 2H4LX 5JMVD 4BACA 3L2VA 4BE0A 1T6AA 3RSMA 3F10A 3OYJA 1VOLB 3OYKA 5IYCP 4EW0A 2QLVA 1UT4A 2LAEA 4EA4A 1YTFA 1E42A 2QREA 2IV8A 5F9CA 1P7MA 3R2XC 2FGTA 4EW4A 2PWWA 3I0XA 2NOZA 4EA5A 1YQMA 5DPKA 2JPIA 2JOIA 5KN8A 4YPRA 1M3QA 1PU6A 3FHGA 1QTSA 4Q11A 2QR1A 3NA5A 3OSTA 1D3UA 3OYBA 1KEAA 3BKQX 1TUOA 1NKUA 2F7LA 5KL0A 4AI4A 4UOBA 1NGNA 3IHOA 4DULA 2EHBD 4ROCB 2NVMA 4OFHA 5EPCA 4BJUA 1QNCA 3RPJA 2V8QA 1UL7A 4ZTFA 3S3OA 1TBAB 4BDYA 4B23A 2JG6A 1DIZA 4UNFA 1VOKA 2NLVA 3OC3C 1N3AA 2NWVA 1YQRA 3L2WA 2Z8UA 1MUYA 2R5XA 3SNSA 1N3CA 4WXAA 3OYMA 3S3NA 4HSBA 3OGDA 3CWTA 3ULXA 4E9EA 1N39A 1QNAA 1KYDA 1KFQA 2I5WA 3OYIA 2W04A 1KG2A 4AI5A 1RRQA 2DKDA 3KRMA 3CVTA 2OOYA 2NOBA 1QN5A 1MPGA 3FHFA 1EUVA 1JFIC 4BDZA 2DKCA 2QRCA 4CFFA 1Q9UA 1KG5A 4OFEA 2MZ8A 1KY7A 1NH2A 5BMPA 1UT7A 4EJYA 1QN3A 2ABKA 2OOXA 3OYFA 2OFIA 4D7RA 3CWSA 1C9BB 2YA3A 4IKFA 2D0BA 1R4XA 2V9JA 4HJHA 1U84A 1KQJA 1KY6A 4B0AA 1KO9A 3DPUA 3C04A 2XHIA 1MP9A 5IYBP 5AN4A 3OYDA 1HU0A 1P5GX 3VN5A 3D4VA 4E9GA 3OH9A 4B22A 2JHNA 3T4NA 1LWVA 3L2QA 3N0UA 1QNBA 1PZDA 2JHJA 1MUDA 2NOFA 4PIIA 1YQLA 4ZTJA 1KG4A 4E9HA 2QRDA 1WEGA 2H5AX 3G0QA 3F0ZA 1KYUA 3CW7A 4EALA 5KN9A 3OY9A 1FN7A 2NOEA 2D0CA 1KYFA 1XG7A 4NZGA 4EAIA 2O3OA 3TE5A 1AISA 4E7IA 2OFKA 4D7QA 2W03A 4OFAA 2V75A 3EIKA 1PU8A 4AIAA 3PDKA 4WZSD 1VTOA 4EVVA 2HKPA 1JDYA 1MUNA 4YOQA 1QN6A 2Y8LA 5CHZA 2FKFA 1YTBA 4C7PA 1PVSA 2Y8QA 1VTLE 3IH7A 3NNQA 3OYHA 2YG8A 5FROA 2G30A 1TBPA 3OS1A 3ENOC 3I0WA 3FSPA 4PY5A 4EAJA 4E7HA 3OYAA 1VKLA 2FKMX 3HS8A 3CVSA 1XQOA 2HL9A 3D7QA 4EAGA 3L2UA 4I8OA 1NVPA 1ORPA 3OSMA 1XQPA 4BE2A 1YQKA 2Z0FA 3LCNA 3OYGA 2YH5A 1NGMA 2HL8A 1VRLA 4E9FA 2NOLA 1LWYA 3OYCA 3OS0A 3OYLA 1RM1A 1QTPA 2YG9A 1XSZA 2MJ7A 3PMGA 1P5DX 5BMNA 2HZMA 1KG6A 1LWWA 2NOHA 4EAKA 3OH6A 3I3WA 3N5NX 1LMZA 4B24A 4EJZA 4YPHA 1PCZA 1LXTA
chains in the Genus database with same CATH topology
2OFKA 4OFAA 1KG2A 3S6IA 1PU8A 4AI5A 4AIAA 1RRQA 4DK9A 3CVTA 2NOBA 3KNTA 1P7MA 4EVVA 1MPGA 1MUNA 3FHFA 4YOQA 4EW4A 3I0XA 1P59A 1KG3A 2NOZA 5CHZA 1KG5A 4OFEA 4EA5A 1YQMA 1PVSA 1ORNA 2H56A 5DPKA 3IH7A 5KN8A 4YPRA 1M3QA 1PU6A 3FHGA 4EJYA 2YG8A 2ABKA 1RRSA 2OFIA 1PU7A 1KG7A 3CWSA 3I0WA 1WEFA 3FSPA 1KEAA 1WEIA 3CVSA 1XQOA 2NOIA 1NKUA 3KTUA 1EBMA 3CWAA 4AI4A 4UOBA 1KQJA 1ORPA 1NGNA 1XQPA 3IHOA 3CWUA 1KO9A 1YQKA 2XHIA 5AN4A 4OFHA 1HU0A 1M3HA 3D4VA 1VRLA 4E9GA 3OH9A 4E9FA 2NOLA 1LWYA 4B22A 2JHNA 4B23A 1LWVA 4B21A 3N0UA 2JG6A 2YG9A 1DIZA 4UNFA 2JHJA 1MUDA 2NOFA 4PIIA 1KG6A 1N3AA 1YQRA 1LWWA 1YQLA 2NOHA 3OH6A 3N5NX 1KG4A 1LMZA 1MUYA 4E9HA 1WEGA 4B24A 3G0QA 3F0ZA 1N3CA 3F10A 4EJZA 4HSBA 3OGDA 3CW7A 4YPHA 3CWTA 4EW0A 5KN9A 4E9EA 1FN7A 2NOEA 1XG7A 1N39A 4EA4A 2I5WA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2OFK A;  4OFA A;  1KG2 A;  3S6I A;  1PU8 A;  4AI5 A;  4AIA A;  1RRQ A;  4DK9 A;  3CVT A;  2NOB A;  3KNT A;  1P7M A;  4EVV A;  1MPG A;  1MUN A;  3FHF A;  4YOQ A;  4EW4 A;  3I0X A;  1P59 A;  1KG3 A;  2NOZ A;  5CHZ A;  1KG5 A;  4OFE A;  4EA5 A;  1YQM A;  1PVS A;  1ORN A;  2H56 A;  5DPK A;  3IH7 A;  5KN8 A;  4YPR A;  1M3Q A;  1PU6 A;  3FHG A;  4EJY A;  2YG8 A;  2ABK A;  1RRS A;  2OFI A;  1PU7 A;  1KG7 A;  3CWS A;  3I0W A;  1WEF A;  3FSP A;  1KEA A;  1WEI A;  3CVS A;  1XQO A;  2NOI A;  1NKU A;  3KTU A;  1EBM A;  3CWA A;  4AI4 A;  4UOB A;  1KQJ A;  1ORP A;  1NGN A;  1XQP A;  3IHO A;  3CWU A;  1KO9 A;  1YQK A;  2XHI A;  5AN4 A;  4OFH A;  1HU0 A;  1M3H A;  3D4V A;  1VRL A;  4E9G A;  3OH9 A;  4E9F A;  2NOL A;  1LWY A;  4B22 A;  2JHN A;  4B23 A;  1LWV A;  4B21 A;  3N0U A;  2JG6 A;  2YG9 A;  1DIZ A;  4UNF A;  2JHJ A;  1MUD A;  2NOF A;  4PII A;  1KG6 A;  1N3A A;  1YQR A;  1LWW A;  1YQL A;  2NOH A;  3OH6 A;  3N5N X;  1KG4 A;  1LMZ A;  1MUY A;  4E9H A;  1WEG A;  4B24 A;  3G0Q A;  3F0Z A;  1N3C A;  3F10 A;  4EJZ A;  4HSB A;  3OGD A;  3CW7 A;  4YPH A;  3CWT A;  4EW0 A;  5KN9 A;  4E9E A;  1FN7 A;  2NOE A;  1XG7 A;  1N39 A;  4EA4 A;  2I5W A; 
#chains in the Genus database with same CATH topology
 4ROE B;  1W80 A;  5FRM A;  1PCM X;  3OSE A;  3S6I A;  1QN7 A;  4ROD B;  4DK9 A;  2DKA A;  3KNT A;  3OS2 A;  1TGH A;  1B9K A;  1WJW A;  1P59 A;  1KG3 A;  4TPS A;  1CDW A;  4WX8 A;  1ORN A;  2H56 A;  1QNE A;  3H1Z A;  3HS9 A;  5HSH A;  3OYN A;  1C47 A;  1J3M A;  3OCI A;  5JN5 A;  5IYD P;  1RRS A;  1PCJ X;  3OLP A;  4E7L A;  1PU7 A;  1KG7 A;  1WEF A;  4IL8 A;  3ASM A;  1WEI A;  2VJ0 A;  2JPS A;  3EAY A;  2NOI A;  1QN4 A;  4QG5 A;  3KTU A;  1EBM A;  1M5Q 1;  3CWA A;  4E7K A;  5FRN A;  3ENC A;  3CWU A;  2ZFD B;  1K35 A;  1M3H A;  1K2Y X;  3L2R A;  3DPT A;  4E7J A;  3VW4 A;  1C4G A;  2HZS A;  3OYE A;  1KFI A;  1WQA A;  3TDH A;  2D0A A;  2IV9 A;  4MRQ A;  4B21 A;  3UW2 A;  4BE1 A;  1QN9 A;  3N89 A;  1V5S A;  2FUV A;  2V92 A;  1QN8 A;  3S3M A;  2H4L X;  5JMV D;  4BAC A;  3L2V A;  4BE0 A;  1T6A A;  3RSM A;  3F10 A;  3OYJ A;  1VOL B;  3OYK A;  5IYC P;  4EW0 A;  2QLV A;  1UT4 A;  2LAE A;  4EA4 A;  1YTF A;  1E42 A;  2QRE A;  2IV8 A;  5F9C A;  1P7M A;  3R2X C;  2FGT A;  4EW4 A;  2PWW A;  3I0X A;  2NOZ A;  4EA5 A;  1YQM A;  5DPK A;  2JPI A;  2JOI A;  5KN8 A;  4YPR A;  1M3Q A;  1PU6 A;  3FHG A;  1QTS A;  4Q11 A;  2QR1 A;  3NA5 A;  3OST A;  1D3U A;  3OYB A;  1KEA A;  3BKQ X;  1TUO A;  1NKU A;  2F7L A;  5KL0 A;  4AI4 A;  4UOB A;  1NGN A;  3IHO A;  4DUL A;  2EHB D;  4ROC B;  2NVM A;  4OFH A;  5EPC A;  4BJU A;  1QNC A;  3RPJ A;  2V8Q A;  1UL7 A;  4ZTF A;  3S3O A;  1TBA B;  4BDY A;  4B23 A;  2JG6 A;  1DIZ A;  4UNF A;  1VOK A;  2NLV A;  3OC3 C;  1N3A A;  2NWV A;  1YQR A;  3L2W A;  2Z8U A;  1MUY A;  2R5X A;  3SNS A;  1N3C A;  4WXA A;  3OYM A;  3S3N A;  4HSB A;  3OGD A;  3CWT A;  3ULX A;  4E9E A;  1N39 A;  1QNA A;  1KYD A;  1KFQ A;  2I5W A;  3OYI A;  2W04 A;  1KG2 A;  4AI5 A;  1RRQ A;  2DKD A;  3KRM A;  3CVT A;  2OOY A;  2NOB A;  1QN5 A;  1MPG A;  3FHF A;  1EUV A;  1JFI C;  4BDZ A;  2DKC A;  2QRC A;  4CFF A;  1Q9U A;  1KG5 A;  4OFE A;  2MZ8 A;  1KY7 A;  1NH2 A;  5BMP A;  1UT7 A;  4EJY A;  1QN3 A;  2ABK A;  2OOX A;  3OYF A;  2OFI A;  4D7R A;  3CWS A;  1C9B B;  2YA3 A;  4IKF A;  2D0B A;  1R4X A;  2V9J A;  4HJH A;  1U84 A;  1KQJ A;  1KY6 A;  4B0A A;  1KO9 A;  3DPU A;  3C04 A;  2XHI A;  1MP9 A;  5IYB P;  5AN4 A;  3OYD A;  1HU0 A;  1P5G X;  3VN5 A;  3D4V A;  4E9G A;  3OH9 A;  4B22 A;  2JHN A;  3T4N A;  1LWV A;  3L2Q A;  3N0U A;  1QNB A;  1PZD A;  2JHJ A;  1MUD A;  2NOF A;  4PII A;  1YQL A;  4ZTJ A;  1KG4 A;  4E9H A;  2QRD A;  1WEG A;  2H5A X;  3G0Q A;  3F0Z A;  1KYU A;  3CW7 A;  4EAL A;  5KN9 A;  3OY9 A;  1FN7 A;  2NOE A;  2D0C A;  1KYF A;  1XG7 A;  4NZG A;  4EAI A;  2O3O A;  3TE5 A;  1AIS A;  4E7I A;  2OFK A;  4D7Q A;  2W03 A;  4OFA A;  2V75 A;  3EIK A;  1PU8 A;  4AIA A;  3PDK A;  4WZS D;  1VTO A;  4EVV A;  2HKP A;  1JDY A;  1MUN A;  4YOQ A;  1QN6 A;  2Y8L A;  5CHZ A;  2FKF A;  1YTB A;  4C7P A;  1PVS A;  2Y8Q A;  1VTL E;  3IH7 A;  3NNQ A;  3OYH A;  2YG8 A;  5FRO A;  2G30 A;  1TBP A;  3OS1 A;  3ENO C;  3I0W A;  3FSP A;  4PY5 A;  4EAJ A;  4E7H A;  3OYA A;  1VKL A;  2FKM X;  3HS8 A;  3CVS A;  1XQO A;  2HL9 A;  3D7Q A;  4EAG A;  3L2U A;  4I8O A;  1NVP A;  1ORP A;  3OSM A;  1XQP A;  4BE2 A;  1YQK A;  2Z0F A;  3LCN A;  3OYG A;  2YH5 A;  1NGM A;  2HL8 A;  1VRL A;  4E9F A;  2NOL A;  1LWY A;  3OYC A;  3OS0 A;  3OYL A;  1RM1 A;  1QTP A;  2YG9 A;  1XSZ A;  2MJ7 A;  3PMG A;  1P5D X;  5BMN A;  2HZM A;  1KG6 A;  1LWW A;  2NOH A;  4EAK A;  3OH6 A;  3I3W A;  3N5N X;  1LMZ A;  4B24 A;  4EJZ A;  4YPH A;  1PCZ A;  1LXT A; 
#chains in the Genus database with same CATH homology
 2OFK A;  4OFA A;  1KG2 A;  3S6I A;  1PU8 A;  4AI5 A;  4AIA A;  1RRQ A;  4DK9 A;  3CVT A;  2NOB A;  3KNT A;  1P7M A;  4EVV A;  1MPG A;  1MUN A;  3FHF A;  4YOQ A;  4EW4 A;  3I0X A;  1P59 A;  1KG3 A;  2NOZ A;  5CHZ A;  1KG5 A;  4OFE A;  4EA5 A;  1YQM A;  1PVS A;  1ORN A;  2H56 A;  5DPK A;  3IH7 A;  5KN8 A;  4YPR A;  1M3Q A;  1PU6 A;  3FHG A;  4EJY A;  2YG8 A;  2ABK A;  1RRS A;  2OFI A;  1PU7 A;  1KG7 A;  3CWS A;  3I0W A;  1WEF A;  3FSP A;  1KEA A;  1WEI A;  3CVS A;  1XQO A;  2NOI A;  1NKU A;  3KTU A;  1EBM A;  3CWA A;  4AI4 A;  4UOB A;  1KQJ A;  1ORP A;  1NGN A;  1XQP A;  3IHO A;  3CWU A;  1KO9 A;  1YQK A;  2XHI A;  5AN4 A;  4OFH A;  1HU0 A;  1M3H A;  3D4V A;  1VRL A;  4E9G A;  3OH9 A;  4E9F A;  2NOL A;  1LWY A;  4B22 A;  2JHN A;  4B23 A;  1LWV A;  4B21 A;  3N0U A;  2JG6 A;  2YG9 A;  1DIZ A;  4UNF A;  2JHJ A;  1MUD A;  2NOF A;  4PII A;  1KG6 A;  1N3A A;  1YQR A;  1LWW A;  1YQL A;  2NOH A;  3OH6 A;  3N5N X;  1KG4 A;  1LMZ A;  1MUY A;  4E9H A;  1WEG A;  4B24 A;  3G0Q A;  3F0Z A;  1N3C A;  3F10 A;  4EJZ A;  4HSB A;  3OGD A;  3CW7 A;  4YPH A;  3CWT A;  4EW0 A;  5KN9 A;  4E9E A;  1FN7 A;  2NOE A;  1XG7 A;  1N39 A;  4EA4 A;  2I5W 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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