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
|
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.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| 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 |
| molecule tags |
Hydrolase/dna
|
| source organism |
Escherichia coli
|
| molecule keywords |
DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3')
|
| 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 |
| 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
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Alpha | Orthogonal Bundle | Endonuclease III; domain 1 | Hypothetical protein; domain 2 | ||
| Mainly Alpha | Orthogonal Bundle | Endonuclease Iii, domain 2 | Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) | ||
| Alpha Beta | 2-Layer Sandwich | TATA-Binding Protein | DNA-3-methyladenine glycosylase AlkA, N-terminal domain |
#chains in the Genus database with same CATH superfamily 3F0Z A; 5CHZ A; 4B21 A; 4B23 A; 2OFK A; 4YPH A; 2OFI A; 1KG3 A; 4E9F A; 1MUD A; 5KN9 A; 1PU8 A; 4EA5 A; 4HSB A; 1YQM A; 2NOI A; 5KN8 A; 3I0W A; 1N3C A; 1N39 A; 2H56 A; 3OH9 A; 3CWS A; 1RRS A; 1M3Q A; 1KG5 A; 4EJZ A; 4OFA A; 3I0X A; 1KG4 A; 1LWW A; 2NOB A; 2JG6 A; 2JHN A; 1VRL A; 1YQK A; 2I5W A; 4DK9 A; 1P59 A; 2NOH A; 3CW7 A; 3FHF A; 3N5N X; 1KG6 A; 2YG9 A; 1KEA A; 3G0Q A; 2NOE A; 1DIZ A; 4YOQ A; 1XQP A; 2NOZ A; 4UNF A; 4PII A; 1YQL A; 4EW4 A; 1MUN A; 3S6I A; 3IHO A; 5DPK A; 4AI5 A; 1LWY A; 1PU7 A; 1PVS A; 1EBM A; 3CVT A; 1NKU A; 1WEG A; 3CWT A; 3FHG A; 3CWU A; 1P7M A; 1XG7 A; 4UOB A; 1ORP A; 3CVS A; 3KNT A; 4AI4 A; 4E9G A; 3N0U A; 4B24 A; 4YPR A; 3OGD A; 1HU0 A; 2YG8 A; 2NOF A; 2JHJ A; 3IH7 A; 3OH6 A; 2ABK A; 1WEI A; 1PU6 A; 1MUY A; 4EA4 A; 3CWA A; 1KO9 A; 2NOL A; 4OFH A; 1NGN A; 1M3H A; 4EVV A; 4E9E A; 1KG7 A; 1KQJ A; 4OFE A; 5AN4 A; 4EW0 A; 1RRQ A; 1LWV A; 1N3A A; 3F10 A; 1KG2 A; 3D4V A; 1YQR A; 3KTU A; 4E9H A; 2XHI A; 4B22 A; 1XQO A; 1FN7 A; 1LMZ A; 1MPG A; 1WEF A; 4EJY A; 4AIA A; 3FSP A; 1ORN A; #chains in the Genus database with same CATH topology 1V5S A; 1VKL A; 4ZTJ A; 2OFK A; 1NGM A; 4YPH A; 1KG3 A; 4B0A A; 3N89 A; 1C4G A; 3T4N A; 2D0C A; 1N3C A; 2JOI A; 3OH9 A; 3OYL A; 3CWS A; 2HL8 A; 1KG5 A; 5KL0 A; 1RM1 A; 2DKC A; 4EAI A; 5IYB P; 2NOB A; 2JG6 A; 1YQK A; 2NOH A; 1P59 A; 1E42 A; 3OS0 A; 1W80 A; 3FHF A; 3N5N X; 3S3N A; 1KG6 A; 2YG9 A; 1KEA A; 2JPS A; 1K35 A; 2JPI A; 4IL8 A; 3UW2 A; 1PCZ A; 1C9B B; 2Y8Q A; 5HSH A; 2G30 A; 4Q11 A; 2NOZ A; 2H5A X; 2FKF A; 1MUN A; 1QNA A; 3ASM A; 3OYD A; 3KRM A; 1Q9U A; 1PU7 A; 1YTB A; 1MP9 A; 1UT7 A; 2QR1 A; 1P7M A; 4UOB A; 4BAC A; 3NNQ A; 1J3M A; 4NZG A; 1KY6 A; 4YPR A; 4ROC B; 3VN5 A; 2YG8 A; 4IKF A; 2NOF A; 3OC3 C; 1XSZ A; 1KYD A; 1T6A A; 4EA4 A; 3CWA A; 4OFH A; 1K2Y X; 1NGN A; 1M3H A; 4EVV A; 4E9E A; 3OYM A; 4QG5 A; 5JMV D; 5AN4 A; 3H1Z A; 2D0A A; 2HL9 A; 2QLV A; 1M5Q 1; 3KTU A; 3ENC A; 4B22 A; 1WQA A; 3PMG A; 2OOY A; 3FSP A; 3OYF A; 3F0Z A; 1PCM X; 2OFI A; 4E9F A; 2R5X A; 1MUD A; 5KN9 A; 3SNS A; 4EA5 A; 2IV9 A; 4D7R A; 2NOI A; 4HJH A; 2FKM X; 3OLP A; 3OYJ A; 1RRS A; 5FRN A; 1QTP A; 5FRO A; 4E7L A; 2V9J A; 4OFA A; 4I8O A; 1QN9 A; 1QN7 A; 3BKQ X; 1LWW A; 2I5W A; 1VRL A; 4DK9 A; 3OYA A; 1D3U A; 4BE2 A; 3OS2 A; 1DIZ A; 4YOQ A; 1XQP A; 3OYG A; 4ROE B; 4UNF A; 4EW4 A; 2QRD A; 3OYC A; 1NVP A; 3L2Q A; 3L2U A; 3VW4 A; 5EPC A; 2DKD A; 1PVS A; 4WZS D; 3FHG A; 5F9C A; 3RSM A; 1ORP A; 3CVS A; 2V75 A; 4E9G A; 3S3O A; 5BMP A; 4EAJ A; 4B24 A; 3L2W A; 3OGD A; 1HU0 A; 2JHJ A; 3OH6 A; 2MJ7 A; 1KFQ A; 1QN6 A; 3D7Q A; 2HZM A; 1KO9 A; 4PY5 A; 2NVM A; 2HZS A; 4BJU A; 1R4X A; 3DPT A; 4EW0 A; 1LWV A; 2Z8U A; 4CFF A; 5IYD P; 3DPU A; 3OY9 A; 1YQR A; 4E9H A; 1XQO A; 3I3W A; 1KY7 A; 5FRM A; 1LMZ A; 4E7J A; 3EIK A; 3HS9 A; 1TUO A; 2QRC A; 2QRE A; 1ORN A; 4B21 A; 2MZ8 A; 1VOK A; 1PU8 A; 4HSB A; 1YQM A; 3OCI A; 5KN8 A; 3I0W A; 1N39 A; 2Y8L A; 5JN5 A; 1M3Q A; 3OYK A; 3ENO C; 1YTF A; 1KG4 A; 2JHN A; 2FUV A; 4BE0 A; 2YA3 A; 3G0Q A; 4E7K A; 2NOE A; 1B9K A; 2OOX A; 1YQL A; 3S6I A; 2F7L A; 3IHO A; 3OYN A; 5DPK A; 4AI5 A; 1LWY A; 1QTS A; 1WEG A; 3OYB A; 3ULX A; 3CWU A; 3OS1 A; 3EAY A; 3HS8 A; 5BMN A; 1QNC A; 4TPS A; 4WXA A; 1KFI A; 3TDH A; 3OYE A; 1MUY A; 1UT4 A; 2DKA A; 3OSM A; 2Z0F A; 3R2X C; 2FGT A; 1C47 A; 1TBA B; 1KQJ A; 4OFE A; 1TGH A; 3F10 A; 2NLV A; 2XHI A; 4E7H A; 3PDK A; 4WX8 A; 1KYU A; 1QN3 A; 2VJ0 A; 4EJY A; 4BE1 A; 1QNB A; 1P5D X; 4AIA A; 1KYF A; 3CVT A; 1VOL B; 5CHZ A; 4B23 A; 4ZTF A; 2W04 A; 1VTL E; 2YH5 A; 1JDY A; 4MRQ A; 1JFI C; 2ZFD B; 3LCN A; 2W03 A; 4C7P A; 4DUL A; 3OSE A; 4D7Q A; 2H56 A; 3S3M A; 2IV8 A; 4EJZ A; 3I0X A; 3L2R A; 3CW7 A; 2V92 A; 3OYI A; 4E7I A; 3C04 A; 3OYH A; 1UL7 A; 2D0B A; 4PII A; 4BDY A; 1QN8 A; 1NH2 A; 2EHB D; 1QN5 A; 2NWV A; 1PZD A; 1EBM A; 1NKU A; 1TBP A; 2PWW A; 1EUV A; 4EAL A; 3CWT A; 1XG7 A; 3OST A; 1VTO A; 2H4L X; 3KNT A; 3RPJ A; 4AI4 A; 1QNE A; 3N0U A; 1CDW A; 4BDZ A; 1LXT A; 3IH7 A; 2ABK A; 2LAE A; 1WEI A; 1WJW A; 1PU6 A; 2NOL A; 1P5G X; 4EAK A; 2V8Q A; 1PCJ X; 4ROD B; 3L2V A; 1QN4 A; 1KG7 A; 2O3O A; 1RRQ A; 2HKP A; 1N3A A; 3NA5 A; 1KG2 A; 3D4V A; 3TE5 A; 4EAG A; 1AIS A; 1FN7 A; 1U84 A; 1MPG A; 1WEF A; 5IYC P; #chains in the Genus database with same CATH homology 3F0Z A; 5CHZ A; 4B21 A; 4B23 A; 2OFK A; 4YPH A; 2OFI A; 1KG3 A; 4E9F A; 1MUD A; 5KN9 A; 1PU8 A; 4EA5 A; 4HSB A; 1YQM A; 2NOI A; 5KN8 A; 3I0W A; 1N3C A; 1N39 A; 2H56 A; 3OH9 A; 3CWS A; 1RRS A; 1M3Q A; 1KG5 A; 4EJZ A; 4OFA A; 3I0X A; 1KG4 A; 1LWW A; 2NOB A; 2JG6 A; 2JHN A; 1VRL A; 1YQK A; 2I5W A; 4DK9 A; 1P59 A; 2NOH A; 3CW7 A; 3FHF A; 3N5N X; 1KG6 A; 2YG9 A; 1KEA A; 3G0Q A; 2NOE A; 1DIZ A; 4YOQ A; 1XQP A; 2NOZ A; 4UNF A; 4PII A; 1YQL A; 4EW4 A; 1MUN A; 3S6I A; 3IHO A; 5DPK A; 4AI5 A; 1LWY A; 1PU7 A; 1PVS A; 1EBM A; 3CVT A; 1NKU A; 1WEG A; 3CWT A; 3FHG A; 3CWU A; 1P7M A; 1XG7 A; 4UOB A; 1ORP A; 3CVS A; 3KNT A; 4AI4 A; 4E9G A; 3N0U A; 4B24 A; 4YPR A; 3OGD A; 1HU0 A; 2YG8 A; 2NOF A; 2JHJ A; 3IH7 A; 3OH6 A; 2ABK A; 1WEI A; 1PU6 A; 1MUY A; 4EA4 A; 3CWA A; 1KO9 A; 2NOL A; 4OFH A; 1NGN A; 1M3H A; 4EVV A; 4E9E A; 1KG7 A; 1KQJ A; 4OFE A; 5AN4 A; 4EW0 A; 1RRQ A; 1LWV A; 1N3A A; 3F10 A; 1KG2 A; 3D4V A; 1YQR A; 3KTU A; 4E9H A; 2XHI A; 4B22 A; 1XQO A; 1FN7 A; 1LMZ A; 1MPG A; 1WEF A; 4EJY A; 4AIA A; 3FSP A; 1ORN A;
#similar chains in the Genus database (?% sequence similarity) ...loading similar chains, please wait... #similar chains, but unknotted ...loading similar chains, please wait... #similar chains in the pdb database (?% sequence similarity) ...loading similar chains, please wait...
