5CFEA

Bacillus subtilis ap endonuclease exoa
Total Genus 83
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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
83
sequence length
252
structure length
252
Chain Sequence
MKLISWNVNGLRAVMRKMDFLSYLKEEDADIICLQETKIQDGQVDLQPEDYHVYWNYAVKKGYSGTAVFSKQEPLQVIYGIGVEEHDQEGRVITLEFENVFVMTVYTPNSRRGLERIDYRMQWEEALLSYILELDQKKPVILCGDLNVAHQEIDLKNPKANRNNAGFSDQEREAFTRFLEAGFVDSFRHVYPDLEGAYSWWSYRAGARDRNIGWRIDYFVVSESLKEQIEDASISADVMGSDHCPVELIINI
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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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publication title Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.
pubmed doi rcsb
molecule tags Hydrolase
source organism Bacillus subtilis (strain 168)
molecule keywords Exodeoxyribonuclease
total genus 83
structure length 252
sequence length 252
ec nomenclature ec 3.1.11.2: Exodeoxyribonuclease III.
pdb deposition date 2015-07-08

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.10.10 Alpha Beta 4-Layer Sandwich Deoxyribonuclease I; Chain A Endonuclease/exonuclease/phosphatase 5cfeA00
2ISIA 3I41A 1I9YA 5J3PA 3NGQA 4LNDA 2JC5A 1WDUA 3MPRA 1SI6X 4FVAA 4L1YA 5EWTA 5J8NA 3I48A 3W2YA 5DFJA 3G0AA 4B5GA 3NR8A 5INQA 3G2DA 4CMLA 4B5JA 2J63A 2F1NA 2UYRX 2DDTA 4L20A 3TEBA 4F1IA 5INNA 2V0SA 2A40B 5DFIA 4GYZA 3G91A 4GZ0A 5CFEA 3G4TA 3MTCA 4JG3A 5J3SA 3NGNA 5DV2A 1NTFA 3FZIA 5INKA 3G6SA 3G3CA 4QH9A 5INLA 3W2XA 4AWNA 3CJCD 5INPA 1DNKA 3W3DB 5A7JA 5DG0A 3L1WA 4GEWA 2IMQX 1VYBA 2XSWA 3N9VA 4A9CA 5DV4A 4GZ2A 5DFHA 2F2FB 2O3HA 3I5VA 3I46A 3G1KA 4CMNA 2A42B 2V0RA 4B5FA 3DNIA 4L1ZA 3K55A 3NGOA 1Y21A 4QHDA 3G8VA 3GA6A 2D1KB 2A3ZB 1I9ZA 4L21A 4IEMA 5CFGA 1AKOA 5HT2A 4F1HB 1DE8A 1SR4B 4RUWA 1ATND 2JC4A 2DDRA 5INMA 3G0RA 3WCXA 3U8UA 2A41B 5DFFA 5A7IA 4K6LF 2O3CA 4C1RA 5J42A 1BIXA 3G3YA 3G38A 4FPVA 5INOA 4B5IA 1YJHA 4B5MA 4B5HA 1HD7A 1ZWXA 4F1HA 3G00A 2VOAA 2DNJA 1DE9A 3G2CA 4F1RA 1E9NA 2DDSA 2EI9A 4PUQA 1DEWA 5J3ZA 4GZ1A 4QHEA
chains in the Genus database with same CATH superfamily
2ISIA 3I41A 1I9YA 5J3PA 3NGQA 4LNDA 2JC5A 1WDUA 3MPRA 1SI6X 4FVAA 4L1YA 5EWTA 5J8NA 3I48A 3W2YA 5DFJA 3G0AA 4B5GA 3NR8A 5INQA 3G2DA 4CMLA 4B5JA 2J63A 2F1NA 2UYRX 2DDTA 4L20A 3TEBA 4F1IA 5INNA 2V0SA 2A40B 5DFIA 4GYZA 3G91A 4GZ0A 5CFEA 3G4TA 3MTCA 4JG3A 5J3SA 3NGNA 5DV2A 1NTFA 3FZIA 5INKA 3G6SA 3G3CA 4QH9A 5INLA 3W2XA 4AWNA 3CJCD 5INPA 1DNKA 3W3DB 5A7JA 5DG0A 3L1WA 4GEWA 2IMQX 1VYBA 2XSWA 3N9VA 4A9CA 5DV4A 4GZ2A 5DFHA 2F2FB 2O3HA 3I5VA 3I46A 3G1KA 4CMNA 2A42B 2V0RA 4B5FA 3DNIA 4L1ZA 3K55A 3NGOA 1Y21A 4QHDA 3G8VA 3GA6A 2D1KB 2A3ZB 1I9ZA 4L21A 4IEMA 5CFGA 1AKOA 5HT2A 4F1HB 1DE8A 1SR4B 4RUWA 1ATND 2JC4A 2DDRA 5INMA 3G0RA 3WCXA 3U8UA 2A41B 5DFFA 5A7IA 4K6LF 2O3CA 4C1RA 5J42A 1BIXA 3G3YA 3G38A 4FPVA 5INOA 4B5IA 1YJHA 4B5MA 4B5HA 1HD7A 1ZWXA 4F1HA 3G00A 2VOAA 2DNJA 1DE9A 3G2CA 4F1RA 1E9NA 2DDSA 2EI9A 4PUQA 1DEWA 5J3ZA 4GZ1A 4QHEA
chains in the Genus database with same CATH topology
2ISIA 3I41A 1I9YA 5J3PA 3NGQA 4LNDA 2JC5A 1WDUA 3MPRA 1SI6X 4FVAA 4L1YA 5EWTA 5J8NA 3I48A 3W2YA 5DFJA 3G0AA 4B5GA 3NR8A 5INQA 3G2DA 4CMLA 4B5JA 2J63A 2F1NA 2UYRX 2DDTA 4L20A 3TEBA 4F1IA 5INNA 2V0SA 2A40B 5DFIA 4GYZA 3G91A 4GZ0A 5CFEA 3G4TA 3MTCA 4JG3A 5J3SA 3NGNA 5DV2A 1NTFA 3FZIA 5INKA 3G6SA 3G3CA 4QH9A 5INLA 3W2XA 4AWNA 3CJCD 5INPA 1DNKA 3W3DB 5A7JA 5DG0A 3L1WA 4GEWA 2IMQX 1VYBA 2XSWA 3N9VA 4A9CA 5DV4A 4GZ2A 5DFHA 2F2FB 2O3HA 3I5VA 3I46A 3G1KA 4CMNA 2A42B 2V0RA 4B5FA 3DNIA 4L1ZA 3K55A 3NGOA 1Y21A 4QHDA 3G8VA 3GA6A 2D1KB 2A3ZB 1I9ZA 4L21A 4IEMA 5CFGA 1AKOA 5HT2A 4F1HB 1DE8A 1SR4B 4RUWA 1ATND 2JC4A 2DDRA 5INMA 3G0RA 3WCXA 3U8UA 2A41B 5DFFA 5A7IA 4K6LF 2O3CA 4C1RA 5J42A 1BIXA 3G3YA 3G38A 4FPVA 5INOA 4B5IA 1YJHA 4B5MA 4B5HA 1HD7A 1ZWXA 4F1HA 3G00A 2VOAA 2DNJA 1DE9A 3G2CA 4F1RA 1E9NA 2DDSA 2EI9A 4PUQA 1DEWA 5J3ZA 4GZ1A 4QHEA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2ISI A;  3I41 A;  1I9Y A;  5J3P A;  3NGQ A;  4LND A;  2JC5 A;  1WDU A;  3MPR A;  1SI6 X;  4FVA A;  4L1Y A;  5EWT A;  5J8N A;  3I48 A;  3W2Y A;  5DFJ A;  3G0A A;  4B5G A;  3NR8 A;  5INQ A;  3G2D A;  4CML A;  4B5J A;  2J63 A;  2F1N A;  2UYR X;  2DDT A;  4L20 A;  3TEB A;  4F1I A;  5INN A;  2V0S A;  2A40 B;  5DFI A;  4GYZ A;  3G91 A;  4GZ0 A;  5CFE A;  3G4T A;  3MTC A;  4JG3 A;  5J3S A;  3NGN A;  5DV2 A;  1NTF A;  3FZI A;  5INK A;  3G6S A;  3G3C A;  4QH9 A;  5INL A;  3W2X A;  4AWN A;  3CJC D;  5INP A;  1DNK A;  3W3D B;  5A7J A;  5DG0 A;  3L1W A;  4GEW A;  2IMQ X;  1VYB A;  2XSW A;  3N9V A;  4A9C A;  5DV4 A;  4GZ2 A;  5DFH A;  2F2F B;  2O3H A;  3I5V A;  3I46 A;  3G1K A;  4CMN A;  2A42 B;  2V0R A;  4B5F A;  3DNI A;  4L1Z A;  3K55 A;  3NGO A;  1Y21 A;  4QHD A;  3G8V A;  3GA6 A;  2D1K B;  2A3Z B;  1I9Z A;  4L21 A;  4IEM A;  5CFG A;  1AKO A;  5HT2 A;  4F1H B;  1DE8 A;  1SR4 B;  4RUW A;  1ATN D;  2JC4 A;  2DDR A;  5INM A;  3G0R A;  3WCX A;  3U8U A;  2A41 B;  5DFF A;  5A7I A;  4K6L F;  2O3C A;  4C1R A;  5J42 A;  1BIX A;  3G3Y A;  3G38 A;  4FPV A;  5INO A;  4B5I A;  1YJH A;  4B5M A;  4B5H A;  1HD7 A;  1ZWX A;  4F1H A;  3G00 A;  2VOA A;  2DNJ A;  1DE9 A;  3G2C A;  4F1R A;  1E9N A;  2DDS A;  2EI9 A;  4PUQ A;  1DEW A;  5J3Z A;  4GZ1 A;  4QHE A; 
#chains in the Genus database with same CATH topology
 2ISI A;  3I41 A;  1I9Y A;  5J3P A;  3NGQ A;  4LND A;  2JC5 A;  1WDU A;  3MPR A;  1SI6 X;  4FVA A;  4L1Y A;  5EWT A;  5J8N A;  3I48 A;  3W2Y A;  5DFJ A;  3G0A A;  4B5G A;  3NR8 A;  5INQ A;  3G2D A;  4CML A;  4B5J A;  2J63 A;  2F1N A;  2UYR X;  2DDT A;  4L20 A;  3TEB A;  4F1I A;  5INN A;  2V0S A;  2A40 B;  5DFI A;  4GYZ A;  3G91 A;  4GZ0 A;  5CFE A;  3G4T A;  3MTC A;  4JG3 A;  5J3S A;  3NGN A;  5DV2 A;  1NTF A;  3FZI A;  5INK A;  3G6S A;  3G3C A;  4QH9 A;  5INL A;  3W2X A;  4AWN A;  3CJC D;  5INP A;  1DNK A;  3W3D B;  5A7J A;  5DG0 A;  3L1W A;  4GEW A;  2IMQ X;  1VYB A;  2XSW A;  3N9V A;  4A9C A;  5DV4 A;  4GZ2 A;  5DFH A;  2F2F B;  2O3H A;  3I5V A;  3I46 A;  3G1K A;  4CMN A;  2A42 B;  2V0R A;  4B5F A;  3DNI A;  4L1Z A;  3K55 A;  3NGO A;  1Y21 A;  4QHD A;  3G8V A;  3GA6 A;  2D1K B;  2A3Z B;  1I9Z A;  4L21 A;  4IEM A;  5CFG A;  1AKO A;  5HT2 A;  4F1H B;  1DE8 A;  1SR4 B;  4RUW A;  1ATN D;  2JC4 A;  2DDR A;  5INM A;  3G0R A;  3WCX A;  3U8U A;  2A41 B;  5DFF A;  5A7I A;  4K6L F;  2O3C A;  4C1R A;  5J42 A;  1BIX A;  3G3Y A;  3G38 A;  4FPV A;  5INO A;  4B5I A;  1YJH A;  4B5M A;  4B5H A;  1HD7 A;  1ZWX A;  4F1H A;  3G00 A;  2VOA A;  2DNJ A;  1DE9 A;  3G2C A;  4F1R A;  1E9N A;  2DDS A;  2EI9 A;  4PUQ A;  1DEW A;  5J3Z A;  4GZ1 A;  4QHE A; 
#chains in the Genus database with same CATH homology
 2ISI A;  3I41 A;  1I9Y A;  5J3P A;  3NGQ A;  4LND A;  2JC5 A;  1WDU A;  3MPR A;  1SI6 X;  4FVA A;  4L1Y A;  5EWT A;  5J8N A;  3I48 A;  3W2Y A;  5DFJ A;  3G0A A;  4B5G A;  3NR8 A;  5INQ A;  3G2D A;  4CML A;  4B5J A;  2J63 A;  2F1N A;  2UYR X;  2DDT A;  4L20 A;  3TEB A;  4F1I A;  5INN A;  2V0S A;  2A40 B;  5DFI A;  4GYZ A;  3G91 A;  4GZ0 A;  5CFE A;  3G4T A;  3MTC A;  4JG3 A;  5J3S A;  3NGN A;  5DV2 A;  1NTF A;  3FZI A;  5INK A;  3G6S A;  3G3C A;  4QH9 A;  5INL A;  3W2X A;  4AWN A;  3CJC D;  5INP A;  1DNK A;  3W3D B;  5A7J A;  5DG0 A;  3L1W A;  4GEW A;  2IMQ X;  1VYB A;  2XSW A;  3N9V A;  4A9C A;  5DV4 A;  4GZ2 A;  5DFH A;  2F2F B;  2O3H A;  3I5V A;  3I46 A;  3G1K A;  4CMN A;  2A42 B;  2V0R A;  4B5F A;  3DNI A;  4L1Z A;  3K55 A;  3NGO A;  1Y21 A;  4QHD A;  3G8V A;  3GA6 A;  2D1K B;  2A3Z B;  1I9Z A;  4L21 A;  4IEM A;  5CFG A;  1AKO A;  5HT2 A;  4F1H B;  1DE8 A;  1SR4 B;  4RUW A;  1ATN D;  2JC4 A;  2DDR A;  5INM A;  3G0R A;  3WCX A;  3U8U A;  2A41 B;  5DFF A;  5A7I A;  4K6L F;  2O3C A;  4C1R A;  5J42 A;  1BIX A;  3G3Y A;  3G38 A;  4FPV A;  5INO A;  4B5I A;  1YJH A;  4B5M A;  4B5H A;  1HD7 A;  1ZWX A;  4F1H A;  3G00 A;  2VOA A;  2DNJ A;  1DE9 A;  3G2C A;  4F1R A;  1E9N A;  2DDS A;  2EI9 A;  4PUQ A;  1DEW A;  5J3Z A;  4GZ1 A;  4QHE 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)

 
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