3D4VA

Crystal structure of an alka host/guest complex n7methylguanine:cytosine base pair
Total Genus 84
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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
84
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 Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Hydrolase/dna
total genus 84
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 2008-05-15

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 3d4vA02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3d4vA03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3d4vA01
4YPRA 5KN9A 1XQPA 3S6IA 4E9EA 1PVSA 1MPGA 4E9FA 5AN4A 1HU0A 1XG7A 1KQJA 4DK9A 3KNTA 2JHNA 4AIAA 1YQMA 4EJYA 3CWUA 3KTUA 1LWVA 1LMZA 4B22A 1N3CA 1KG5A 1RRSA 1KG3A 1XQOA 3OGDA 2OFIA 3I0XA 4OFAA 2YG8A 4EA4A 3F0ZA 1VRLA 1YQKA 1LWYA 3F10A 5DPKA 4YOQA 4HSBA 2NOHA 4AI4A 1FN7A 1NGNA 1ORNA 1WEFA 3CVSA 4OFEA 3CWTA 2OFKA 1WEIA 1KG6A 3CW7A 4B21A 1WEGA 4YPHA 2NOBA 3CVTA 1NKUA 4EJZA 1P59A 1KG7A 1MUNA 1N39A 3OH9A 1KEAA 3G0QA 1YQLA 1MUYA 4EA5A 2NOEA 2NOIA 1KG2A 3FHGA 2YG9A 1PU8A 1ORPA 4E9HA 4EW4A 2JG6A 4OFHA 4B24A 1DIZA 3OH6A 1PU6A 3CWAA 1MUDA 1KG4A 1PU7A 3FHFA 4AI5A 2NOLA 1RRQA 1LWWA 4E9GA 3CWSA 3N5NX 2I5WA 1YQRA 4EVVA 3FSPA 3D4VA 4EW0A 1P7MA 2ABKA 5KN8A 4UNFA 4B23A 3IH7A 1M3HA 3N0UA 4PIIA 1KO9A 2H56A 2NOZA 5CHZA 1M3QA 3IHOA 2NOFA 1N3AA 2XHIA 2JHJA 1EBMA 4UOBA 3I0WA
chains in the Genus database with same CATH superfamily
4YPRA 3OS1A 1VKLA 5KN9A 3S3MA 2F7LA 1XQPA 2NLVA 1VOLB 2FGTA 3PMGA 2NVMA 1PVSA 1WQAA 1HU0A 2IV9A 3H1ZA 3KNTA 3S3OA 3OS0A 3TE5A 1YQMA 4MRQA 4EAGA 4D7QA 1LMZA 4B22A 4WZSD 2W04A 1N3CA 1U84A 1KFQA 2FUVA 4QG5A 3OYGA 4EA4A 2V92A 3OYFA 3TDHA 3RSMA 5DPKA 4YOQA 2HL8A 1NGNA 2D0AA 2DKCA 3ENOC 3CW7A 1YTFA 4B21A 2NOBA 3OYLA 3L2RA 1C47A 3HS8A 1QNEA 3OYBA 1KG2A 1JDYA 1NVPA 2NWVA 5JN5A 3VW4A 2G30A 4BDZA 2HZMA 2JG6A 3S3NA 3OH6A 3L2UA 3L2VA 3CWAA 1MUDA 4E7IA 2O3OA 1LWWA 4E9GA 1CDWA 3N5NX 2Z8UA 1P5GX 3PDKA 5BMNA 2V8QA 3OYIA 5IYCP 2JPIA 4UNFA 3IH7A 4PIIA 2H56A 3SNSA 1M3QA 3NNQA 2QRDA 5FRNA 2NOFA 1VTOA 1D3UA 1WJWA 1EBMA 1KYDA 4UOBA 1W80A 5AN4A 4EAIA 2FKMX 2JHNA 5KL0A 4AIAA 1V5SA 4EAJA 4EJYA 1KY6A 3CWUA 4DULA 2QREA 1RRSA 1KG3A 2OFIA 1QN6A 4OFAA 2YG8A 3F0ZA 4PY5A 1KYUA 3F10A 1UT7A 4CFFA 3RPJA 1UT4A 1WEFA 2LAEA 1K35A 3NA5A 1NH2A 3CVSA 4OFEA 1WEIA 1KG6A 1WEGA 3OYAA 1NKUA 4EJZA 1P59A 1JFIC 4BDYA 1N39A 1YQLA 4BE0A 4D7RA 4E7HA 4BACA 4EA5A 3DPTA 3FHGA 2YG9A 4NZGA 1E42A 1PU8A 3OYEA 4EALA 4E9HA 4EW4A 3OSTA 1QN7A 4OFHA 3EIKA 4E7JA 1PU6A 1VOKA 4BE1A 3OC3C 1UL7A 1MP9A 3CWSA 1XSZA 3VN5A 4EAKA 1YTBA 1KFIA 1C9BB 3R2XC 2I5WA 1YQRA 3ASMA 5FROA 3D7QA 4BJUA 3OYCA 3FSPA 4EW0A 4RODB 1QTPA 4IL8A 4ROCB 4B23A 1KO9A 1NGMA 1N3AA 2QRCA 4B0AA 3BKQX 1QTSA 4E7LA 1QNAA 2YA3A 3C04A 4E9FA 1TBAB 4I8OA 1XG7A 3OYKA 4WXAA 1EUVA 5HSHA 4HJHA 4Q11A 3KTUA 3OSMA 2R5XA 3KRMA 1TUOA 3OGDA 2Y8LA 2ZFDB 1AISA 1QN5A 2QR1A 1YQKA 1LWYA 2MZ8A 4HSBA 2NOHA 1FN7A 1VTLE 2H5AX 2V9JA 4C7PA 3EAYA 2VJ0A 3DPUA 4ZTJA 1P5DX 3OYHA 2OFKA 3OYJA 5IYBP 3OH9A 1KEAA 3G0QA 5JMVD 1TBPA 2HKPA 1QN9A 1M5Q1 4IKFA 2NOEA 2NOIA 2D0CA 1PZDA 2DKAA 1ORPA 3L2QA 4TPSA 4B24A 1DIZA 4BE2A 3OYDA 1QN4A 4WX8A 2OOYA 1KG4A 1PU7A 3FHFA 2NOLA 1RRQA 2H4LX 1KY7A 2W03A 3D4VA 4ROEB 3OCIA 2EHBD 1P7MA 3OSEA 5KN8A 2FKFA 3ULXA 2Y8QA 3T4NA 1QNBA 2NOZA 1PCMX 3N89A 2JHJA 3IHOA 3S6IA 4E9EA 2IV8A 1MPGA 1KQJA 4ZTFA 4DK9A 2PWWA 3OLPA 3OYMA 1Q9UA 2DKDA 2HZSA 2Z0FA 4E7KA 1KYFA 1LWVA 1LXTA 1KG5A 2YH5A 1XQOA 3I0XA 2JOIA 3ENCA 3OY9A 1VRLA 4AI4A 1ORNA 1QN3A 2HL9A 3CWTA 4YPHA 1B9KA 1R4XA 3CVTA 1TGHA 3HS9A 2JPSA 1KG7A 3UW2A 1MUNA 5EPCA 3OYNA 1MUYA 5F9CA 1PCJX 3LCNA 1QNCA 1C4GA 2MJ7A 2OOXA 4AI5A 5BMPA 2V75A 1PCZA 2QLVA 3OS2A 2D0BA 4EVVA 2ABKA 5IYDP 5FRMA 1J3MA 1M3HA 3N0UA 1QN8A 1K2YX 3I3WA 5CHZA 2XHIA 1RM1A 3L2WA 1T6AA 3I0WA
chains in the Genus database with same CATH topology
4YPRA 5KN9A 1XQPA 3S6IA 4E9EA 1PVSA 1MPGA 4E9FA 5AN4A 1HU0A 1XG7A 1KQJA 4DK9A 3KNTA 2JHNA 4AIAA 1YQMA 4EJYA 3CWUA 3KTUA 1LWVA 1LMZA 4B22A 1N3CA 1KG5A 1RRSA 1KG3A 1XQOA 3OGDA 2OFIA 3I0XA 4OFAA 2YG8A 4EA4A 3F0ZA 1VRLA 1YQKA 1LWYA 3F10A 5DPKA 4YOQA 4HSBA 2NOHA 4AI4A 1FN7A 1NGNA 1ORNA 1WEFA 3CVSA 4OFEA 3CWTA 2OFKA 1WEIA 1KG6A 3CW7A 4B21A 1WEGA 4YPHA 2NOBA 3CVTA 1NKUA 4EJZA 1P59A 1KG7A 1MUNA 1N39A 3OH9A 1KEAA 3G0QA 1YQLA 1MUYA 4EA5A 2NOEA 2NOIA 1KG2A 3FHGA 2YG9A 1PU8A 1ORPA 4E9HA 4EW4A 2JG6A 4OFHA 4B24A 1DIZA 3OH6A 1PU6A 3CWAA 1MUDA 1KG4A 1PU7A 3FHFA 4AI5A 2NOLA 1RRQA 1LWWA 4E9GA 3CWSA 3N5NX 2I5WA 1YQRA 4EVVA 3FSPA 3D4VA 4EW0A 1P7MA 2ABKA 5KN8A 4UNFA 4B23A 3IH7A 1M3HA 3N0UA 4PIIA 1KO9A 2H56A 2NOZA 5CHZA 1M3QA 3IHOA 2NOFA 1N3AA 2XHIA 2JHJA 1EBMA 4UOBA 3I0WA
chains in the Genus database with same CATH homology


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