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


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