3OGDA

Alka undamaged dna complex: interrogation of a g*:c base pair
Total Genus 87

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
87
sequence length
288
structure length
288
Chain Sequence
MADIGSEFYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQCVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDE

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
3H1 (65-70)S1 (0-5)3H2 (96-99)AH1 (12-22)AH3 (88-95)EMPTYTII1 (24-27)S2 (28-31)TII2 (123-126)AH6 (158-163)TIV2 (31-34)S3 (34-41)S4 (44-53)TIV3 (40-43)TI2 (54-57)TI1 (53-56)AH4 (113-123)TI6 (149-152)AH2 (71-82)S5 (58-63)TI3 (83-86)TIV4 (99-102)TVIII1 (100-103)TI4 (102-105)AH5 (128-142)TI5 (146-149)AH8 (176-191)S6 (144-145)TIV5 (147-150)S7 (153-154)AH7 (166-172)AH9 (202-211)TI7 (235-238)TII3 (212-215)AH10 (217-228)TIV7 (243-246)AH11 (239-243)TIV8 (245-248)TI8 (257-260)TVIa1 (260-263)AH13 (264-273)TIV6 (230-233)TVIII2 (192-195)TVIII3 (199-202)AH12 (251-257)TI9 (274-277)Updating...
connected with : NaN
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 87
structure length 288
sequence length 288
ec nomenclature ec 3.2.2.21: DNA-3-methyladenine glycosylase II.
pdb deposition date 2010-08-16

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 3ogdA02
1.10.1670.10 Mainly Alpha Orthogonal Bundle Endonuclease Iii, domain 2 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) 3ogdA03
3.30.310.20 Alpha Beta 2-Layer Sandwich TATA-Binding Protein DNA-3-methyladenine glycosylase AlkA, N-terminal domain 3ogdA01
1XQOA 3CW7A 4B23A 1N3AA 4EW4A 1YQKA 1LWWA 1MUNA 1KG7A 2NOHA 4OFEA 2JHNA 3F0ZA 1ORNA 1WEIA 1KG2A 3CVTA 3FHFA 3CWAA 1ORPA 2H56A 3I0WA 4E9GA 1KG5A 2OFKA 1KG3A 4HSBA 4E9HA 2I5WA 1MPGA 3OH9A 1YQLA 3D4VA 1N39A 1M3HA 1FN7A 3IHOA 2NOLA 4AI5A 1XQPA 3N5NX 1PU8A 1NGNA 1WEGA 2ABKA 4AIAA 1XG7A 4AI4A 2NOIA 4E9EA 4EJZA 5DPKA 3CWTA 3OGDA 4EVVA 1YQMA 4UNFA 1KO9A 1YQRA 4OFAA 1P7MA 2NOEA 1MUDA 3FHGA 4B22A 3KNTA 1DIZA 1M3QA 2YG8A 1KEAA 1MUYA 3CWUA 4OFHA 1VRLA 3IH7A 1LWVA 4PIIA 1NKUA 4EJYA 1KQJA 4EA5A 3I0XA 3KTUA 5KN9A 1HU0A 4E9FA 3OH6A 4DK9A 3S6IA 3G0QA 4EA4A 2NOFA 4EW0A 4B24A 5CHZA 1LMZA 4UOBA 4YPRA 1N3CA 1RRSA 4YOQA 1PU6A 1KG4A 2JG6A 2NOBA 3FSPA 2JHJA 3F10A 2OFIA 2YG9A 5KN8A 1PVSA 1LWYA 3CVSA 1WEFA 4B21A 1P59A 3N0UA 1EBMA 1PU7A 2XHIA 1KG6A 3CWSA 2NOZA 5AN4A 4YPHA 1RRQA
chains in the Genus database with same CATH superfamily
1EUVA 5HSHA 4CFFA 1LWWA 2HL9A 4OFEA 2Y8LA 3NNQA 1AISA 1XSZA 3CWAA 3I0WA 2QRCA 5F9CA 3BKQX 2OFKA 1KG3A 4HSBA 4C7PA 1MPGA 3ASMA 1VKLA 4BE0A 1E42A 1VOKA 1VOLB 3IHOA 1PCZA 2YH5A 1XQPA 3N5NX 3R2XC 2ABKA 4ROEB 3OSMA 3L2QA 2IV9A 1QNAA 4EJZA 3OGDA 3OCIA 3OSTA 1VTOA 4BDYA 1VTLE 4OFAA 1P7MA 2PWWA 4IL8A 1MUYA 3OSEA 3CWUA 1VRLA 1KY6A 3PDKA 4WZSD 4EA5A 1V5SA 4EAGA 1QN3A 3ULXA 4EAKA 1JDYA 3KRMA 3HS8A 4I8OA 2W04A 4WX8A 4DK9A 3S6IA 2Z8UA 1QN5A 2JPIA 4UOBA 2NVMA 1KG4A 1M5Q1 3OYIA 1C47A 1TBAB 4MRQA 2DKDA 4B0AA 2QREA 2YG9A 2D0BA 2Z0FA 5KN8A 3OYJA 1NH2A 3N0UA 3OS2A 4D7RA 2HZMA 2XHIA 3OYBA 2W03A 2QLVA 3RSMA 5BMNA 1KFQA 3S3NA 4B23A 4EW4A 4BE1A 1P5DX 1PCMX 1K2YX 1WEIA 3CVTA 1QNBA 1KY7A 2YA3A 1CDWA 1M3HA 1QN7A 4E7IA 2NOLA 3OYMA 1QN8A 3T4NA 2MZ8A 3OYFA 3OC3C 4AIAA 4AI4A 2NOIA 4E9EA 1B9KA 3CWTA 1QNEA 1YQMA 4UNFA 1KO9A 1YQRA 5IYBP 1DIZA 3OLPA 2V9JA 1LXTA 1LWVA 5FROA 3KTUA 3OYAA 3SNSA 2VJ0A 3EIKA 4E9FA 2H5AX 1W80A 1QN4A 2V92A 3G0QA 4IKFA 1LMZA 4YPRA 2F7LA 1MP9A 1RRSA 4E7KA 2R5XA 1PU6A 4PY5A 2JG6A 2FKFA 5JMVD 5IYDP 4RODB 3LCNA 2JHJA 2NWVA 5KL0A 1LWYA 4BDZA 4ZTJA 3DPTA 1EBMA 4HJHA 1KG6A 3CWSA 2JPSA 1U84A 5AN4A 4YPHA 1RRQA 1XQOA 3CW7A 1N3AA 1YQKA 2HZSA 4BACA 1WJWA 2NLVA 3I3WA 1UL7A 2JHNA 2HKPA 1QN9A 1J3MA 1KG2A 4BE2A 2H56A 4E9GA 4DULA 3OYHA 2O3OA 3L2VA 1KG5A 1QTSA 4E9HA 2I5WA 2DKAA 4D7QA 5IYCP 3OH9A 1QNCA 1YQLA 1N39A 1FN7A 4AI5A 2FKMX 2ZFDB 1QTPA 3ENCA 1KYFA 5DPKA 3VW4A 4EVVA 3OYEA 1MUDA 1UT7A 3FHGA 1P5GX 1R4XA 2QR1A 2YG8A 1KEAA 4OFHA 2OOXA 1PCJX 1NKUA 4EJYA 3I0XA 5KN9A 4BJUA 3OS1A 3OH6A 3RPJA 4EA4A 2NOFA 4QG5A 4EW0A 4B24A 5CHZA 4E7LA 2MJ7A 4ROCB 3L2RA 2NOBA 1C9BB 3L2UA 1YTFA 2OFIA 3OS0A 3CVSA 2FUVA 4EAIA 4B21A 1P59A 3OYDA 3OYGA 1KYUA 2NOZA 3TDHA 1JFIC 5FRNA 2FGTA 3UW2A 1KFIA 1MUNA 3DPUA 1KG7A 2NOHA 3F0ZA 1TBPA 2H4LX 1QN6A 1ORNA 1T6AA 3S3MA 2LAEA 1YTBA 4WXAA 3FHFA 5EPCA 4ZTFA 1ORPA 3OYLA 2G30A 5JN5A 3L2WA 3D4VA 4Q11A 2D0CA 1PU8A 1NGNA 1WEGA 3VN5A 1XG7A 3EAYA 3C04A 2Y8QA 3OYNA 3PMGA 3S3OA 3D7QA 4E7JA 1Q9UA 2NOEA 1C4GA 4EALA 1D3UA 4B22A 3KNTA 1M3QA 3IH7A 1NVPA 5BMPA 2JOIA 4PIIA 1KQJA 5FRMA 1HU0A 3H1ZA 4NZGA 3NA5A 2D0AA 4TPSA 1KYDA 2IV8A 2EHBD 1WQAA 2V75A 1N3CA 3OYCA 4YOQA 2HL8A 3N89A 1NGMA 3HS9A 3FSPA 3OY9A 2DKCA 4E7HA 3F10A 3TE5A 3OYKA 1PVSA 1WEFA 1K35A 3ENOC 1RM1A 1TUOA 2V8QA 1PU7A 2OOYA 1UT4A 2QRDA 4EAJA 1TGHA 1PZDA
chains in the Genus database with same CATH topology
1XQOA 3CW7A 4B23A 1N3AA 4EW4A 1YQKA 1LWWA 1MUNA 1KG7A 2NOHA 4OFEA 2JHNA 3F0ZA 1ORNA 1WEIA 1KG2A 3CVTA 3FHFA 3CWAA 1ORPA 2H56A 3I0WA 4E9GA 1KG5A 2OFKA 1KG3A 4HSBA 4E9HA 2I5WA 1MPGA 3OH9A 1YQLA 3D4VA 1N39A 1M3HA 1FN7A 3IHOA 2NOLA 4AI5A 1XQPA 3N5NX 1PU8A 1NGNA 1WEGA 2ABKA 4AIAA 1XG7A 4AI4A 2NOIA 4E9EA 4EJZA 5DPKA 3CWTA 3OGDA 4EVVA 1YQMA 4UNFA 1KO9A 1YQRA 4OFAA 1P7MA 2NOEA 1MUDA 3FHGA 4B22A 3KNTA 1DIZA 1M3QA 2YG8A 1KEAA 1MUYA 3CWUA 4OFHA 1VRLA 3IH7A 1LWVA 4PIIA 1NKUA 4EJYA 1KQJA 4EA5A 3I0XA 3KTUA 5KN9A 1HU0A 4E9FA 3OH6A 4DK9A 3S6IA 3G0QA 4EA4A 2NOFA 4EW0A 4B24A 5CHZA 1LMZA 4UOBA 4YPRA 1N3CA 1RRSA 4YOQA 1PU6A 1KG4A 2JG6A 2NOBA 3FSPA 2JHJA 3F10A 2OFIA 2YG9A 5KN8A 1PVSA 1LWYA 3CVSA 1WEFA 4B21A 1P59A 3N0UA 1EBMA 1PU7A 2XHIA 1KG6A 3CWSA 2NOZA 5AN4A 4YPHA 1RRQA
chains in the Genus database with same CATH homology


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