3OH9A

Alka undamaged dna complex: interrogation of a t:a 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
288
structure length
288
Chain Sequence
MADIGSEFYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDCLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDE
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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 tags Hydrolase/dna
source organism Escherichia coli
publication title Structure of Escherichia coli AlkA in Complex with Undamaged DNA.
pubmed doi rcsb
molecule keywords DNA-3-methyladenine glycosylase 2
total genus 84
structure length 288
sequence length 288
ec nomenclature ec 3.2.2.21: DNA-3-methyladenine glycosylase II.
pdb deposition date 2010-08-17

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 3oh9A02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3oh9A03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3oh9A01
1LMZA 3KNTA 4PIIA 1KG2A 2ABKA 3CWSA 1ORPA 3IHOA 1WEGA 1KQJA 1YQRA 1MPGA 3CWUA 1M3QA 1N39A 1PU7A 1P59A 2NOLA 1KO9A 3IH7A 5KN8A 2I5WA 2OFKA 1PVSA 4EJZA 3OGDA 2JHJA 2YG9A 1ORNA 1PU6A 2NOEA 1XG7A 3CWTA 5KN9A 1XQPA 3CW7A 4DK9A 1P7MA 3OH9A 1LWVA 4OFAA 2OFIA 4EA4A 4E9EA 4YPRA 3N0UA 4B23A 4EW0A 1MUDA 4AIAA 3CVTA 2NOIA 1PU8A 4B22A 2NOHA 1KG7A 3D4VA 1DIZA 1WEFA 1RRQA 1YQMA 2YG8A 1N3AA 1MUYA 2JG6A 1WEIA 4AI4A 1MUNA 4AI5A 1NGNA 2XHIA 4OFHA 5DPKA 1RRSA 3F0ZA 3KTUA 3CWAA 1VRLA 1FN7A 4UNFA 2NOFA 1KEAA 3FHFA 2NOBA 2H56A 3CVSA 4E9HA 1N3CA 1EBMA 1KG6A 2JHNA 1KG3A 3F10A 4EVVA 2NOZA 4OFEA 1LWWA 3S6IA 4YOQA 3OH6A 4B21A 5CHZA 5AN4A 1LWYA 3N5NX 1KG5A 4UOBA 1KG4A 3FHGA 1XQOA 4EW4A 1M3HA 4EJYA 1YQKA 3FSPA 4E9GA 3I0WA 4B24A 4E9FA 4EA5A 4HSBA 1HU0A 1NKUA 1YQLA 3I0XA 3G0QA 4YPHA
chains in the Genus database with same CATH superfamily
1LMZA 4I8OA 1VOLB 2V92A 1KG2A 2NVMA 5IYBP 2ABKA 3LCNA 3OCIA 3L2VA 1YQRA 4B0AA 1KY6A 2H4LX 2R5XA 1KFIA 2F7LA 1TBAB 1QTSA 4D7RA 2NOLA 4E7HA 1KO9A 3IH7A 4QG5A 2I5WA 2DKCA 3OGDA 5KL0A 2QRCA 1XSZA 5KN9A 3NA5A 2QR1A 4DK9A 1UL7A 1PCMX 1QNBA 4BE2A 2FKMX 1NH2A 3OYIA 4B23A 1MUDA 4B22A 1KG7A 3R2XC 3OS1A 1RRQA 5BMPA 3OYLA 4C7PA 2PWWA 1QNAA 4WX8A 3DPTA 2OOXA 1MUNA 1AISA 2MZ8A 2XHIA 4OFHA 5FROA 1RRSA 3HS8A 2DKDA 3KTUA 1VRLA 1WQAA 2HL9A 2G30A 1KEAA 1M5Q1 4E9HA 5FRNA 2VJ0A 3D7QA 1QN8A 2YA3A 4EVVA 3S3NA 4OFEA 1LWWA 2W03A 3S6IA 1J3MA 3N5NX 1QN3A 1KG4A 3FHGA 1XQOA 3S3MA 4WZSD 2QLVA 1JDYA 4B24A 4E7KA 4EA5A 1QN7A 3OYHA 3ENCA 1TGHA 4D7QA 5EPCA 1KYDA 3ASMA 3TE5A 1E42A 1QTPA 2Y8QA 2JPSA 2JOIA 1YTBA 2MJ7A 2D0BA 2O3OA 4CFFA 1MPGA 1M3QA 2JPIA 1MP9A 4PY5A 1N39A 2W04A 2H5AX 3T4NA 5KN8A 3UW2A 2OFKA 5IYCP 1QNCA 2YG9A 1PU6A 2NOEA 1XG7A 3CWTA 2Z8UA 4EAJA 4ROEB 3L2UA 3CW7A 2HKPA 4OFAA 1T6AA 4EA4A 4EAKA 3HS9A 3N0UA 2NOIA 3I3WA 1PU8A 3ENOC 1K2YX 3VW4A 1YQMA 1QN6A 5IYDP 1JFIC 2IV8A 4BJUA 3SNSA 5JN5A 4AI4A 3OYGA 1NGMA 3OSEA 3OSTA 1B9KA 5JMVD 4BACA 4BE0A 3L2QA 3CWAA 3L2RA 2Z0FA 4WXAA 1EBMA 1KG6A 1KG3A 3F10A 2Y8LA 5HSHA 1LWYA 1VKLA 1K35A 3OYMA 2D0AA 3OC3C 2V9JA 1YQKA 3FSPA 4E9FA 4E7JA 3PDKA 1YQLA 3I0XA 3G0QA 4YPHA 3NNQA 3KNTA 2HZMA 2QRDA 4PIIA 1VTLE 3OS0A 1ORPA 3IHOA 3CWUA 4IL8A 4BDYA 1C4GA 1PVSA 4EJZA 2NWVA 1PCZA 2DKAA 2JHJA 2HL8A 3VN5A 1C9BB 1KY7A 1P7MA 3OH9A 1LWVA 1VTOA 2OFIA 4E9EA 4YPRA 4ZTFA 5FRMA 3OYBA 1D3UA 4EW0A 1W80A 3CVTA 2NOHA 1DIZA 3OLPA 1MUYA 2JG6A 4BE1A 1WEIA 2V8QA 3OYAA 3L2WA 4AI5A 1NGNA 3OYCA 1QN5A 2LAEA 1PCJX 3EIKA 3F0ZA 1UT7A 1QNEA 3H1ZA 4UNFA 2NOFA 4E7IA 1KYFA 3S3OA 2NOBA 3CVSA 4NZGA 4YOQA 3OH6A 2ZFDB 4BDZA 4EW4A 3I0WA 4EAIA 2EHBD 4HSBA 2FUVA 1NKUA 4EAGA 1C47A 2IV9A 3OYDA 2D0CA 2YH5A 4Q11A 2FKFA 3C04A 3RSMA 3CWSA 1WEGA 5BMNA 1KQJA 4ZTJA 3RPJA 1V5SA 1PU7A 3BKQX 1P59A 3TDHA 2OOYA 3OS2A 3OYKA 1PZDA 4EALA 1ORNA 1LXTA 1QN9A 1XQPA 3EAYA 1P5DX 2FGTA 5F9CA 1U84A 4RODB 4TPSA 2V75A 4AIAA 3OY9A 1NVPA 3D4VA 3N89A 1WEFA 3PMGA 4IKFA 2YG8A 1N3AA 3OYFA 2QREA 3OYNA 3ULXA 1P5GX 3OYJA 1KFQA 1TUOA 5DPKA 1VOKA 4MRQA 1WJWA 1FN7A 2HZSA 3FHFA 2H56A 1N3CA 3DPUA 4DULA 2JHNA 2NOZA 4B21A 1CDWA 5CHZA 5AN4A 1Q9UA 1UT4A 1R4XA 1KG5A 4UOBA 2NLVA 1EUVA 1TBPA 3OYEA 1M3HA 4EJYA 3OSMA 4E9GA 1KYUA 4ROCB 3KRMA 1HU0A 1QN4A 4HJHA 1YTFA 4E7LA 1RM1A
chains in the Genus database with same CATH topology
1LMZA 3KNTA 4PIIA 1KG2A 2ABKA 3CWSA 1ORPA 3IHOA 1WEGA 1KQJA 1YQRA 1MPGA 3CWUA 1M3QA 1N39A 1PU7A 1P59A 2NOLA 1KO9A 3IH7A 5KN8A 2I5WA 2OFKA 1PVSA 4EJZA 3OGDA 2JHJA 2YG9A 1ORNA 1PU6A 2NOEA 1XG7A 3CWTA 5KN9A 1XQPA 3CW7A 4DK9A 1P7MA 3OH9A 1LWVA 4OFAA 2OFIA 4EA4A 4E9EA 4YPRA 3N0UA 4B23A 4EW0A 1MUDA 4AIAA 3CVTA 2NOIA 1PU8A 4B22A 2NOHA 1KG7A 3D4VA 1DIZA 1WEFA 1RRQA 1YQMA 2YG8A 1N3AA 1MUYA 2JG6A 1WEIA 4AI4A 1MUNA 4AI5A 1NGNA 2XHIA 4OFHA 5DPKA 1RRSA 3F0ZA 3KTUA 3CWAA 1VRLA 1FN7A 4UNFA 2NOFA 1KEAA 3FHFA 2NOBA 2H56A 3CVSA 4E9HA 1N3CA 1EBMA 1KG6A 2JHNA 1KG3A 3F10A 4EVVA 2NOZA 4OFEA 1LWWA 3S6IA 4YOQA 3OH6A 4B21A 5CHZA 5AN4A 1LWYA 3N5NX 1KG5A 4UOBA 1KG4A 3FHGA 1XQOA 4EW4A 1M3HA 4EJYA 1YQKA 3FSPA 4E9GA 3I0WA 4B24A 4E9FA 4EA5A 4HSBA 1HU0A 1NKUA 1YQLA 3I0XA 3G0QA 4YPHA
chains in the Genus database with same CATH homology


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