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


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