1DIZA

Crystal structure of e. coli 3-methyladenine dna glycosylase (alka) complexed with dna
Total Genus 93
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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
93
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 (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3')
publication title DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Hydrolase/dna
total genus 93
structure length 282
sequence length 282
chains with identical sequence B
ec nomenclature ec 3.2.2.21: DNA-3-methyladenine glycosylase II.
pdb deposition date 1999-11-30

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 1dizA02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 1dizA03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 1dizA01
1N3AA 3CVTA 1XQOA 1P7MA 2I5WA 4PIIA 4EW0A 1YQMA 4E9GA 4E9EA 4EVVA 1NGNA 1LWYA 1YQRA 2NOIA 2ABKA 1M3HA 2NOLA 1MPGA 1KO9A 3CWUA 3I0WA 1XQPA 1EBMA 3CWAA 2XHIA 4EA5A 4YOQA 3OGDA 1MUNA 3N0UA 1HU0A 2NOHA 1KG5A 1KEAA 2JG6A 3FSPA 1WEGA 4YPHA 1FN7A 1M3QA 1KQJA 1YQLA 1PU7A 5CHZA 5DPKA 1P59A 4YPRA 3F10A 4UOBA 1VRLA 1WEIA 2NOFA 1XG7A 4OFAA 4EA4A 2NOZA 3CVSA 4OFHA 1RRQA 1ORNA 1KG7A 2JHJA 2OFKA 3CWTA 4B24A 3D4VA 1MUDA 3IHOA 1LWVA 3S6IA 4HSBA 5KN8A 5AN4A 5KN9A 4AI5A 3FHFA 1LWWA 3CWSA 3CW7A 1DIZA 1RRSA 3FHGA 3I0XA 4E9FA 1ORPA 2NOEA 2OFIA 4UNFA 1PU6A 1LMZA 1KG4A 1PVSA 4E9HA 1N39A 1N3CA 4EJZA 3KNTA 1KG3A 4B23A 2YG8A 1YQKA 4AI4A 4B21A 2YG9A 4B22A 4EJYA 1NKUA 3OH6A 2JHNA 4EW4A 4DK9A 2NOBA 1WEFA 4OFEA 3N5NX 3KTUA 3IH7A 1MUYA 3OH9A 1KG2A 1KG6A 4AIAA 1PU8A 2H56A 3F0ZA 3G0QA
chains in the Genus database with same CATH superfamily
3OYKA 4IL8A 1XQOA 1P7MA 5FRMA 2NWVA 4E9EA 4WZSD 3ENOC 3H1ZA 2ABKA 2OOXA 4BACA 4ZTFA 5IYCP 1KO9A 3S3OA 3TDHA 2V9JA 1K2YX 3OS0A 3LCNA 1MUNA 3N0UA 3OYLA 1UL7A 4BDYA 3R2XC 3EIKA 1M3QA 3D7QA 1KQJA 3L2WA 5HSHA 1PU7A 3BKQX 1MP9A 5CHZA 2G30A 4EAGA 4UOBA 2NOFA 1WEIA 2EHBD 4EA4A 2NOZA 4OFHA 2OFKA 3D4VA 1C9BB 1MUDA 1QNBA 1NGMA 3OYMA 4QG5A 2D0AA 1QN5A 1LWWA 2Y8LA 3CWSA 3OCIA 1QN7A 2QLVA 2IV9A 4WX8A 2H4LX 3RPJA 3S3NA 2VJ0A 5EPCA 2HKPA 4IKFA 4EJZA 2QRDA 3KNTA 4B23A 1YQKA 1QN3A 4AI4A 3I3WA 2YH5A 4EJYA 3OSTA 4EW4A 4OFEA 3OYFA 3OYBA 4RODB 1MUYA 3OH9A 1VOKA 1KG2A 3OYDA 1PU8A 2W03A 2H56A 1CDWA 1LXTA 1QTPA 1NVPA 2NLVA 1R4XA 2I5WA 4BE0A 4E9GA 4EVVA 1YQRA 5JN5A 4EAJA 3OLPA 4E7JA 3HS8A 1TUOA 3CWUA 5FROA 4EAIA 1EBMA 2HZMA 2Y8QA 2XHIA 4YOQA 3OGDA 1HU0A 4PY5A 5JMVD 3ULXA 1KG5A 1KEAA 2JG6A 1TGHA 1WEGA 3OYGA 2QREA 1FN7A 3VN5A 1NH2A 1YQLA 4Q11A 2F7LA 3OY9A 1YTFA 3CVSA 1RRQA 1ORNA 4WXAA 4DULA 1KG7A 3CWTA 4B24A 1EUVA 1WJWA 3L2QA 3IHOA 4E7KA 1C4GA 2HL9A 2D0CA 5KN8A 3HS9A 1UT4A 3FHFA 1KYFA 2FGTA 3ENCA 1RRSA 3PDKA 4CFFA 1KY7A 4EALA 3NA5A 1PU6A 3PMGA 1KG4A 4C7PA 2HZSA 2O3OA 3TE5A 3L2VA 1YTBA 2YG8A 2HL8A 4B22A 1NKUA 4D7RA 1PCJX 2JHNA 2NOBA 1P5GX 3UW2A 3IH7A 1VOLB 1PCZA 3RSMA 2NVMA 2D0BA 4E7IA 2Z8UA 4BJUA 2JPIA 3F0ZA 3L2RA 1N3AA 3CVTA 1YQMA 2FKFA 1NGNA 2QRCA 2FUVA 3C04A 2NOLA 3OS1A 1K35A 1QN9A 2FKMX 2PWWA 1PZDA 3OYEA 3CWAA 2MZ8A 2DKDA 2NOHA 5IYBP 3FSPA 4YPHA 1AISA 1QN6A 2Z0FA 1VTOA 3VW4A 1P59A 1VTLE 1XG7A 3L2UA 4OFAA 1P5DX 1JFIC 3T4NA 4E7LA 4EAKA 4ROEB 1KYDA 3OYJA 1QTSA 2OOYA 3S6IA 2YA3A 1M5Q1 5KL0A 5AN4A 5KN9A 1QNEA 3OS2A 1DIZA 2LAEA 1ORPA 1RM1A 4ZTJA 2NOEA 2JOIA 3OYHA 1KFIA 3N89A 5F9CA 1KY6A 2OFIA 3ASMA 4I8OA 2ZFDB 4E9HA 2DKCA 3OYIA 1QNCA 1E42A 2YG9A 4BDZA 3OH6A 4ROCB 2V75A 1WEFA 3OC3C 3N5NX 3EAYA 4BE1A 2JPSA 1TBAB 3OYCA 4AIAA 1QN4A 1KYUA 3NNQA 3G0QA 4MRQA 4TPSA 1VKLA 4PIIA 4EW0A 2R5XA 5IYDP 1LWYA 2H5AX 5FRNA 1QN8A 2NOIA 1M3HA 1C47A 1MPGA 1Q9UA 3I0WA 1XQPA 2DKAA 4EA5A 3SNSA 1J3MA 3OYNA 5DPKA 4YPRA 3F10A 1VRLA 1QNAA 3DPTA 1T6AA 1UT7A 2JHJA 1W80A 3OYAA 1LWVA 4NZGA 2V92A 4D7QA 4HSBA 1D3UA 3KRMA 1B9KA 1U84A 4AI5A 3CW7A 2V8QA 4E7HA 3S3MA 2IV8A 1JDYA 3FHGA 3I0XA 4E9FA 1TBPA 3DPUA 1V5SA 3OSEA 4UNFA 1LMZA 1N39A 1PVSA 1WQAA 1N3CA 1XSZA 1KG3A 2MJ7A 4B0AA 4B21A 1PCMX 4BE2A 5BMPA 2W04A 4HJHA 4DK9A 1KFQA 3OSMA 3KTUA 2QR1A 5BMNA 1KG6A
chains in the Genus database with same CATH topology
1N3AA 3CVTA 1XQOA 1P7MA 2I5WA 4PIIA 4EW0A 1YQMA 4E9GA 4E9EA 4EVVA 1NGNA 1LWYA 1YQRA 2NOIA 2ABKA 1M3HA 2NOLA 1MPGA 1KO9A 3CWUA 3I0WA 1XQPA 1EBMA 3CWAA 2XHIA 4EA5A 4YOQA 3OGDA 1MUNA 3N0UA 1HU0A 2NOHA 1KG5A 1KEAA 2JG6A 3FSPA 1WEGA 4YPHA 1FN7A 1M3QA 1KQJA 1YQLA 1PU7A 5CHZA 5DPKA 1P59A 4YPRA 3F10A 4UOBA 1VRLA 1WEIA 2NOFA 1XG7A 4OFAA 4EA4A 2NOZA 3CVSA 4OFHA 1RRQA 1ORNA 1KG7A 2JHJA 2OFKA 3CWTA 4B24A 3D4VA 1MUDA 3IHOA 1LWVA 3S6IA 4HSBA 5KN8A 5AN4A 5KN9A 4AI5A 3FHFA 1LWWA 3CWSA 3CW7A 1DIZA 1RRSA 3FHGA 3I0XA 4E9FA 1ORPA 2NOEA 2OFIA 4UNFA 1PU6A 1LMZA 1KG4A 1PVSA 4E9HA 1N39A 1N3CA 4EJZA 3KNTA 1KG3A 4B23A 2YG8A 1YQKA 4AI4A 4B21A 2YG9A 4B22A 4EJYA 1NKUA 3OH6A 2JHNA 4EW4A 4DK9A 2NOBA 1WEFA 4OFEA 3N5NX 3KTUA 3IH7A 1MUYA 3OH9A 1KG2A 1KG6A 4AIAA 1PU8A 2H56A 3F0ZA 3G0QA
chains in the Genus database with same CATH homology


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