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


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