3CW7A

Crystal structure of an alka host/guest complex 8oxoguanine:cytosine base pair
Total Genus 88
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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
88
sequence length
282
structure length
282
Chain Sequence
MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA
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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 the E. coli DNA Glycosylase AlkA Bound to the Ends of Duplex DNA: A System for the Structure Determination of Lesion-Containing DNA.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Hydrolase/dna
molecule keywords DNA-3-methyladenine glycosylase 2
total genus 88
structure length 282
sequence length 282
chains with identical sequence B, C, D
ec nomenclature ec 3.2.2.21: DNA-3-methyladenine glycosylase II.
pdb deposition date 2008-04-21

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein
A PF06029 AlkA_N AlkA N-terminal domain
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 3cw7A02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3cw7A03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3cw7A01
5AN4A 3KTUA 1LWVA 1KG2A 1KEAA 4UOBA 3IH7A 1KG6A 2NOIA 1PU6A 1KO9A 1XG7A 2YG9A 5KN8A 3OH6A 4B24A 4EJYA 2YG8A 3I0XA 3CWUA 1RRQA 1N39A 3F10A 1KG3A 2NOLA 1KG7A 4YPHA 3OGDA 1MUDA 2NOHA 1N3CA 2ABKA 4OFAA 2NOEA 4B23A 1NGNA 3I0WA 3CVTA 4E9FA 1WEIA 1WEFA 3FHGA 3N5NX 1XQOA 4E9GA 1NKUA 1DIZA 1M3QA 2NOZA 3KNTA 1N3AA 3G0QA 1YQKA 4EW0A 1RRSA 2OFKA 4DK9A 1HU0A 5CHZA 4PIIA 1KG5A 1P59A 1YQMA 2XHIA 2OFIA 2NOFA 2H56A 4OFHA 1WEGA 1VRLA 1PVSA 1YQRA 1YQLA 4EA5A 4EVVA 2JG6A 3CVSA 4OFEA 1M3HA 4E9EA 2JHJA 1KG4A 3CWTA 5KN9A 1EBMA 4HSBA 3FSPA 1ORNA 1ORPA 2NOBA 5DPKA 4UNFA 1PU7A 2I5WA 1LMZA 1LWYA 1MUYA 4AIAA 4B22A 3FHFA 3IHOA 1P7MA 1PU8A 4E9HA 1MUNA 1MPGA 4YPRA 4YOQA 4AI5A 4EA4A 3OH9A 3F0ZA 4AI4A 1LWWA 3CWSA 3S6IA 4B21A 1FN7A 2JHNA 3D4VA 3CWAA 4EW4A 1XQPA 3CW7A 1KQJA 3N0UA 4EJZA
chains in the Genus database with same CATH superfamily
2FKMX 1PCJX 5FRNA 3OYHA 2FGTA 2HZSA 2EHBD 2QRDA 4NZGA 1KYDA 3S3OA 5KN8A 1UT4A 3OH6A 3I0XA 4ROEB 2NOLA 1K35A 3OYBA 3OGDA 2NOHA 1PCMX 2ABKA 1KY7A 4B23A 1NGNA 2YH5A 2DKDA 4BE2A 5JMVD 1WEIA 3FHGA 4E9GA 5JN5A 2D0AA 2V9JA 4TPSA 2H5AX 3G0QA 4WX8A 1D3UA 1YQKA 2QREA 1KG5A 2OOYA 2OFIA 4BE1A 1NH2A 4BJUA 4HJHA 1VRLA 3OYCA 1UT7A 3OLPA 5KL0A 2DKAA 3OYJA 4E9EA 2PWWA 1RM1A 1TBPA 3CWTA 3VW4A 1QNBA 2G30A 4UNFA 3OYNA 1KYUA 1PU7A 3D7QA 1LWYA 4B0AA 5IYDP 1K2YX 1P7MA 1PU8A 1QTSA 1QN4A 1MUNA 2H4LX 2YA3A 3F0ZA 1TBAB 2V8QA 3LCNA 1LWWA 3CWSA 4B21A 5FRMA 1FN7A 2NVMA 1QN6A 4E7HA 3OSMA 5AN4A 1VTLE 4UOBA 3NNQA 3IH7A 1LXTA 1UL7A 1KG6A 1AISA 1XG7A 1KO9A 3OYLA 3CWUA 1B9KA 1VOKA 5IYCP 1KG7A 2IV8A 4YPHA 3OSEA 2NOEA 1M5Q1 3R2XC 1WEFA 1YTBA 3N5NX 3HS8A 1TUOA 5BMNA 4IKFA 1QTPA 3ENOC 2LAEA 4EW0A 1HU0A 2MJ7A 4BACA 2NOFA 3OYKA 2H56A 5HSHA 1NVPA 1WEGA 1KYFA 1YQRA 3CVSA 2MZ8A 3OYIA 1M3HA 3OS2A 4E7IA 3FSPA 5EPCA 1LMZA 1MUYA 4AIAA 1MPGA 4YPRA 4YOQA 3PDKA 2FKFA 4AI5A 4E7LA 3ASMA 3D4VA 1XQPA 3CW7A 3OCIA 3N0UA 1TGHA 3L2RA 5BMPA 4PY5A 2O3OA 2ZFDB 1KEAA 1W80A 2HL8A 3ULXA 1QNAA 1VKLA 1JFIC 3S3NA 2R5XA 3DPTA 1PU6A 2YG9A 1VTOA 2YG8A 3OS1A 3L2QA 3DPUA 1RRQA 2DKCA 1Q9UA 3EAYA 3N89A 3HS9A 4CFFA 1N3CA 2D0BA 3TE5A 4EAKA 1WJWA 3CVTA 3I0WA 4D7RA 1PZDA 1C47A 3H1ZA 1VOLB 1XQOA 2W03A 1DIZA 1PCZA 2HZMA 2NOZA 3UW2A 4MRQA 4EALA 3RSMA 2HL9A 1QNEA 4PIIA 1MP9A 5IYBP 2XHIA 2QLVA 1QN8A 4OFHA 3PMGA 3OSTA 3OYEA 1YQLA 2JG6A 5FROA 2Y8LA 4E7JA 1C9BB 4WXAA 5F9CA 1E42A 4BDYA 3VN5A 4EAJA 2QRCA 3OYFA 3S3MA 1ORPA 2NLVA 2NOBA 3L2UA 5DPKA 2I5WA 3IHOA 4E9HA 1KFQA 2JOIA 2W04A 1NGMA 2D0CA 3OH9A 4AI4A 2FUVA 4ZTFA 4C7PA 3CWAA 3OY9A 3KRMA 1QN5A 3KTUA 1CDWA 1LWVA 2IV9A 1KG2A 1WQAA 1QN3A 1P5GX 3L2VA 3T4NA 2NOIA 4EJYA 4B24A 4Q11A 1U84A 4BDZA 1J3MA 4E7KA 2V92A 4D7QA 1N39A 3F10A 1KG3A 2JPIA 3OS0A 3OYAA 1KFIA 1QN7A 4DULA 2V75A 2VJ0A 3OYGA 1MUDA 4OFAA 1R4XA 4ZTJA 3EIKA 4E9FA 1C4GA 1NKUA 4BE0A 1M3QA 1EUVA 1T6AA 3KNTA 1N3AA 1QN9A 1V5SA 2JPSA 4QG5A 1XSZA 1RRSA 2OFKA 4DK9A 5CHZA 2Z0FA 2HKPA 3OYDA 1P59A 4IL8A 1YQMA 3SNSA 3TDHA 3C04A 2F7LA 1PVSA 1YTFA 3OC3C 4EA5A 4EVVA 2OOXA 4OFEA 3NA5A 2JHJA 2NWVA 1KG4A 4ROCB 5KN9A 1EBMA 4HSBA 1ORNA 1QNCA 2Y8QA 3ENCA 4B22A 3FHFA 3OYMA 4EAIA 3RPJA 1KY6A 4EA4A 3L2WA 2QR1A 3BKQX 4RODB 2Z8UA 1P5DX 3S6IA 2JHNA 3I3WA 4WZSD 4EW4A 1JDYA 4I8OA 4EAGA 1KQJA 4EJZA
chains in the Genus database with same CATH topology
5AN4A 3KTUA 1LWVA 1KG2A 1KEAA 4UOBA 3IH7A 1KG6A 2NOIA 1PU6A 1KO9A 1XG7A 2YG9A 5KN8A 3OH6A 4B24A 4EJYA 2YG8A 3I0XA 3CWUA 1RRQA 1N39A 3F10A 1KG3A 2NOLA 1KG7A 4YPHA 3OGDA 1MUDA 2NOHA 1N3CA 2ABKA 4OFAA 2NOEA 4B23A 1NGNA 3I0WA 3CVTA 4E9FA 1WEIA 1WEFA 3FHGA 3N5NX 1XQOA 4E9GA 1NKUA 1DIZA 1M3QA 2NOZA 3KNTA 1N3AA 3G0QA 1YQKA 4EW0A 1RRSA 2OFKA 4DK9A 1HU0A 5CHZA 4PIIA 1KG5A 1P59A 1YQMA 2XHIA 2OFIA 2NOFA 2H56A 4OFHA 1WEGA 1VRLA 1PVSA 1YQRA 1YQLA 4EA5A 4EVVA 2JG6A 3CVSA 4OFEA 1M3HA 4E9EA 2JHJA 1KG4A 3CWTA 5KN9A 1EBMA 4HSBA 3FSPA 1ORNA 1ORPA 2NOBA 5DPKA 4UNFA 1PU7A 2I5WA 1LMZA 1LWYA 1MUYA 4AIAA 4B22A 3FHFA 3IHOA 1P7MA 1PU8A 4E9HA 1MUNA 1MPGA 4YPRA 4YOQA 4AI5A 4EA4A 3OH9A 3F0ZA 4AI4A 1LWWA 3CWSA 3S6IA 4B21A 1FN7A 2JHNA 3D4VA 3CWAA 4EW4A 1XQPA 3CW7A 1KQJA 3N0UA 4EJZA
chains in the Genus database with same CATH homology


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