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


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