3CVTA

Crystal structure of an alka host/guest complex 8oxoguanine:cytosine base pair
Total Genus 85
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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
85
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
molecule keywords DNA-3-methyladenine glycosylase 2
molecule tags Hydrolase/dna
source organism Escherichia coli
total genus 85
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 2008-04-19

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 3cvtA02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3cvtA03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3cvtA01
1KQJA 4UNFA 3F10A 2JHJA 3F0ZA 1DIZA 4AIAA 1N3CA 4B24A 1KEAA 2I5WA 4B22A 1WEFA 4PIIA 1ORPA 4OFEA 1WEGA 1WEIA 4YPRA 1ORNA 3OGDA 3CVSA 1LWYA 4OFAA 3CWAA 1VRLA 5CHZA 1KG4A 1KG2A 3I0XA 1MUDA 4B21A 1M3HA 1NKUA 3CW7A 1MUNA 1P59A 1P7MA 2OFIA 1PU6A 3N5NX 1NGNA 1XQOA 1KG3A 2ABKA 4EW4A 5AN4A 5DPKA 2NOHA 3S6IA 1PU8A 1YQMA 2YG9A 2XHIA 4EA5A 3IH7A 3CWSA 4E9HA 4EVVA 1LWVA 1MPGA 1YQRA 1EBMA 3IHOA 4UOBA 3FSPA 4E9FA 4EW0A 1RRSA 1XG7A 2NOLA 3OH9A 1PVSA 1YQLA 4AI4A 4HSBA 3CWTA 4YOQA 2JG6A 1YQKA 1HU0A 2OFKA 3N0UA 3CVTA 4B23A 3FHFA 4YPHA 4EA4A 2NOIA 1KG5A 1KG6A 4DK9A 2NOFA 4E9EA 2NOBA 3KNTA 3D4VA 1M3QA 2YG8A 1N3AA 1RRQA 4OFHA 1PU7A 4EJZA 3OH6A 5KN9A 2NOEA 3G0QA 1XQPA 1FN7A 1LMZA 2NOZA 5KN8A 1N39A 4AI5A 1KG7A 2H56A 4E9GA 1MUYA 1KO9A 3KTUA 2JHNA 3I0WA 3CWUA 3FHGA 1LWWA 4EJYA
chains in the Genus database with same CATH superfamily
3OCIA 3OY9A 1LXTA 2DKDA 4EAGA 4E7KA 3F10A 1U84A 2JHJA 3OYAA 1MP9A 2I5WA 4WZSD 2MJ7A 1QNAA 3OS0A 3OC3C 3OYGA 4OFEA 1B9KA 1QN7A 2H5AX 4I8OA 1KYUA 1KG4A 1KG2A 4E7LA 3OS2A 4NZGA 2MZ8A 1QN9A 2DKAA 1UT4A 4BDZA 5DPKA 5AN4A 1K2YX 2YG9A 4Q11A 2NVMA 1KYDA 2FUVA 3L2VA 2G30A 1TGHA 3R2XC 4EAJA 2D0CA 4DULA 2Y8LA 2HL8A 4UOBA 5HSHA 5EPCA 1WQAA 2IV9A 1RRSA 2NOLA 2FKFA 3OYJA 3CWTA 2D0BA 1UL7A 2V92A 2VJ0A 3FHFA 4YPHA 2PWWA 4QG5A 1KG5A 1KG6A 4DK9A 2NOBA 2YG8A 4BE0A 1YTFA 4ZTFA 2NWVA 5JN5A 3VN5A 2HL9A 1NVPA 1QTPA 4E9GA 3OYKA 3L2QA 1QN8A 2W03A 1C47A 3VW4A 2H4LX 3CWUA 3OSEA 2JPIA 1CDWA 3HS8A 4BJUA 3F0ZA 1DIZA 1N3CA 1KEAA 1NGMA 4B22A 1WEFA 3RSMA 1ORPA 1QNCA 4YPRA 1WEIA 3EIKA 3OGDA 4B0AA 1KFQA 1NH2A 1D3UA 3CWAA 4EAIA 1UT7A 1Q9UA 5CHZA 1V5SA 3OYDA 2EHBD 3OYHA 2V9JA 3CW7A 1MUNA 4RODB 2V75A 1P7MA 2W04A 3ASMA 3I3WA 4BE1A 1PU8A 1QN6A 3BKQX 2Z0FA 3ENCA 1K35A 3IH7A 4IL8A 4E9HA 4EVVA 1R4XA 1WJWA 1MPGA 1YQRA 5BMNA 3IHOA 2D0AA 4E9FA 3H1ZA 4AI4A 1KFIA 2JG6A 1YQKA 2Y8QA 2OFKA 3C04A 2JPSA 1PZDA 2YH5A 3N0UA 3CVTA 4EA4A 3S3NA 1VOKA 2QLVA 3D4VA 2NLVA 3TDHA 1RRQA 4OFHA 1PU7A 3OYLA 3G0QA 3ULXA 2LAEA 1QN5A 5KN8A 4WXAA 4MRQA 1TUOA 3OS1A 5F9CA 4E7HA 1KO9A 3N89A 3OYCA 4IKFA 4BDYA 1PCJX 3I0WA 4BE2A 3FHGA 1LWWA 2QR1A 2O3OA 4EALA 3UW2A 1J3MA 1RM1A 5IYDP 4HJHA 5FRMA 3HS9A 2ZFDB 4PIIA 2Z8UA 3S3OA 1VKLA 1WEGA 3CVSA 4D7QA 4OFAA 3OYIA 1TBPA 3I0XA 5JMVD 1MUDA 4B21A 2OFIA 3N5NX 1NGNA 1KG3A 2ABKA 1P5DX 4EW4A 2XHIA 1LWVA 1KY6A 1EBMA 3NNQA 5IYBP 4TPSA 1QNBA 3SNSA 1XG7A 3OH9A 1YQLA 1P5GX 4HSBA 2OOYA 1EUVA 1HU0A 3OYNA 2HZMA 2FKMX 4B23A 4PY5A 3OYEA 2NOIA 2NOFA 2OOXA 4E9EA 3KNTA 1M3QA 1QN3A 1JFIC 3DPTA 1JDYA 2NOEA 1XQPA 5FRNA 1AISA 1FN7A 4E7IA 3PMGA 4D7RA 4AI5A 3PDKA 1KG7A 3DPUA 1MUYA 1VTOA 3KTUA 2V8QA 1YTBA 2HKPA 1VOLB 3L2WA 4EJYA 2QRDA 1M5Q1 3EAYA 1KQJA 1C4GA 4UNFA 2YA3A 5BMPA 1PCMX 4AIAA 1PCZA 4B24A 1VTLE 4ZTJA 1ORNA 3D7QA 1QTSA 5KL0A 1LWYA 3KRMA 4CFFA 1VRLA 1KYFA 1C9BB 5FROA 1M3HA 1NKUA 3TE5A 1P59A 1PU6A 3OSTA 1TBAB 3OYFA 1XQOA 4E7JA 3LCNA 2NOHA 3S6IA 1YQMA 4EA5A 4ROCB 3S3MA 3CWSA 1XSZA 2F7LA 4EAKA 1KY7A 3FSPA 3L2UA 4EW0A 1QNEA 1PVSA 4BACA 3RPJA 3OSMA 1T6AA 4YOQA 3L2RA 2QRCA 2IV8A 1E42A 2QREA 4WX8A 5IYCP 1N3AA 2JOIA 4EJZA 3T4NA 3OH6A 5KN9A 3OYMA 4ROEB 3OYBA 1LMZA 2NOZA 2DKCA 2FGTA 1N39A 2HZSA 2H56A 1W80A 2R5XA 3OLPA 2JHNA 1QN4A 4C7PA 3NA5A 3ENOC
chains in the Genus database with same CATH topology
1KQJA 4UNFA 3F10A 2JHJA 3F0ZA 1DIZA 4AIAA 1N3CA 4B24A 1KEAA 2I5WA 4B22A 1WEFA 4PIIA 1ORPA 4OFEA 1WEGA 1WEIA 4YPRA 1ORNA 3OGDA 3CVSA 1LWYA 4OFAA 3CWAA 1VRLA 5CHZA 1KG4A 1KG2A 3I0XA 1MUDA 4B21A 1M3HA 1NKUA 3CW7A 1MUNA 1P59A 1P7MA 2OFIA 1PU6A 3N5NX 1NGNA 1XQOA 1KG3A 2ABKA 4EW4A 5AN4A 5DPKA 2NOHA 3S6IA 1PU8A 1YQMA 2YG9A 2XHIA 4EA5A 3IH7A 3CWSA 4E9HA 4EVVA 1LWVA 1MPGA 1YQRA 1EBMA 3IHOA 4UOBA 3FSPA 4E9FA 4EW0A 1RRSA 1XG7A 2NOLA 3OH9A 1PVSA 1YQLA 4AI4A 4HSBA 3CWTA 4YOQA 2JG6A 1YQKA 1HU0A 2OFKA 3N0UA 3CVTA 4B23A 3FHFA 4YPHA 4EA4A 2NOIA 1KG5A 1KG6A 4DK9A 2NOFA 4E9EA 2NOBA 3KNTA 3D4VA 1M3QA 2YG8A 1N3AA 1RRQA 4OFHA 1PU7A 4EJZA 3OH6A 5KN9A 2NOEA 3G0QA 1XQPA 1FN7A 1LMZA 2NOZA 5KN8A 1N39A 4AI5A 1KG7A 2H56A 4E9GA 1MUYA 1KO9A 3KTUA 2JHNA 3I0WA 3CWUA 3FHGA 1LWWA 4EJYA
chains in the Genus database with same CATH homology


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