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


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