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


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