1DE9A

Human ape1 endonuclease with bound abasic dna and mn2+ ion
Total Genus 80
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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
80
sequence length
276
structure length
276
Chain Sequence
ALYEDPPDHKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
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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 DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
pubmed doi rcsb
molecule tags Lyase/dna
source organism Homo sapiens
molecule keywords 5'-d(*CP*TP*AP*C)-3'
total genus 80
structure length 276
sequence length 276
chains with identical sequence B
ec nomenclature ec 4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
pdb deposition date 1999-11-13

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 1de9A00
2A40B 4L20A 5DV4A 1WDUA 3K55A 4QHDA 3I5VA 1I9YA 2D1KB 5DFJA 5DG0A 4L21A 2UYRX 5CFEA 3G0AA 2J63A 4QH9A 5INPA 5EWTA 3MTCA 3W2YA 2DNJA 2DDSA 3G0RA 3WCXA 1SI6X 5INNA 1YJHA 3NGQA 4C1RA 5J3SA 2V0SA 1SR4B 4B5GA 3I41A 2A42B 4GZ0A 2IMQX 5HT2A 3G2DA 5INMA 3G38A 2VOAA 5DV2A 5J42A 5INLA 3G91A 5INOA 5DFHA 5INKA 1Y21A 4B5MA 3G1KA 4B5IA 1I9ZA 2F2FB 3W2XA 4F1HA 1BIXA 3GA6A 4GZ2A 4GZ1A 2ISIA 4F1IA 3NGOA 2A41B 5J3ZA 2F1NA 1DE8A 5A7IA 5DFIA 4PUQA 1AKOA 3N9VA 3G8VA 3TEBA 4B5FA 4AWNA 1NTFA 4QHEA 1DNKA 5A7JA 2EI9A 2DDRA 2O3HA 2XSWA 2DDTA 1VYBA 4B5HA 3G3YA 3NGNA 1E9NA 3U8UA 4B5JA 2JC5A 4GYZA 4L1YA 2JC4A 4IEMA 4FVAA 2A3ZB 4RUWA 3G2CA 2V0RA 5DFFA 4A9CA 3I48A 3G6SA 4L1ZA 4LNDA 4CMLA 4GEWA 4FPVA 3G4TA 3G00A 5J3PA 1ATND 3L1WA 1DE9A 1ZWXA 3CJCD 3I46A 5J8NA 4JG3A 5INQA 3DNIA 4CMNA 3W3DB 1DEWA 3NR8A 3FZIA 5CFGA 4F1RA 4K6LF 3G3CA 4F1HB 1HD7A 2O3CA 3MPRA
chains in the Genus database with same CATH superfamily
2A40B 4L20A 5DV4A 1WDUA 3K55A 4QHDA 3I5VA 1I9YA 2D1KB 5DFJA 5DG0A 4L21A 2UYRX 5CFEA 3G0AA 2J63A 4QH9A 5INPA 5EWTA 3MTCA 3W2YA 2DNJA 2DDSA 3G0RA 3WCXA 1SI6X 5INNA 1YJHA 3NGQA 4C1RA 5J3SA 2V0SA 1SR4B 4B5GA 3I41A 2A42B 4GZ0A 2IMQX 5HT2A 3G2DA 5INMA 3G38A 2VOAA 5DV2A 5J42A 5INLA 3G91A 5INOA 5DFHA 5INKA 1Y21A 4B5MA 3G1KA 4B5IA 1I9ZA 2F2FB 3W2XA 4F1HA 1BIXA 3GA6A 4GZ2A 4GZ1A 2ISIA 4F1IA 3NGOA 2A41B 5J3ZA 2F1NA 1DE8A 5A7IA 5DFIA 4PUQA 1AKOA 3N9VA 3G8VA 3TEBA 4B5FA 4AWNA 1NTFA 4QHEA 1DNKA 5A7JA 2EI9A 2DDRA 2O3HA 2XSWA 2DDTA 1VYBA 4B5HA 3G3YA 3NGNA 1E9NA 3U8UA 4B5JA 2JC5A 4GYZA 4L1YA 2JC4A 4IEMA 4FVAA 2A3ZB 4RUWA 3G2CA 2V0RA 5DFFA 4A9CA 3I48A 3G6SA 4L1ZA 4LNDA 4CMLA 4GEWA 4FPVA 3G4TA 3G00A 5J3PA 1ATND 3L1WA 1DE9A 1ZWXA 3CJCD 3I46A 5J8NA 4JG3A 5INQA 3DNIA 4CMNA 3W3DB 1DEWA 3NR8A 3FZIA 5CFGA 4F1RA 4K6LF 3G3CA 4F1HB 1HD7A 2O3CA 3MPRA
chains in the Genus database with same CATH topology
2A40B 4L20A 5DV4A 1WDUA 3K55A 4QHDA 3I5VA 1I9YA 2D1KB 5DFJA 5DG0A 4L21A 2UYRX 5CFEA 3G0AA 2J63A 4QH9A 5INPA 5EWTA 3MTCA 3W2YA 2DNJA 2DDSA 3G0RA 3WCXA 1SI6X 5INNA 1YJHA 3NGQA 4C1RA 5J3SA 2V0SA 1SR4B 4B5GA 3I41A 2A42B 4GZ0A 2IMQX 5HT2A 3G2DA 5INMA 3G38A 2VOAA 5DV2A 5J42A 5INLA 3G91A 5INOA 5DFHA 5INKA 1Y21A 4B5MA 3G1KA 4B5IA 1I9ZA 2F2FB 3W2XA 4F1HA 1BIXA 3GA6A 4GZ2A 4GZ1A 2ISIA 4F1IA 3NGOA 2A41B 5J3ZA 2F1NA 1DE8A 5A7IA 5DFIA 4PUQA 1AKOA 3N9VA 3G8VA 3TEBA 4B5FA 4AWNA 1NTFA 4QHEA 1DNKA 5A7JA 2EI9A 2DDRA 2O3HA 2XSWA 2DDTA 1VYBA 4B5HA 3G3YA 3NGNA 1E9NA 3U8UA 4B5JA 2JC5A 4GYZA 4L1YA 2JC4A 4IEMA 4FVAA 2A3ZB 4RUWA 3G2CA 2V0RA 5DFFA 4A9CA 3I48A 3G6SA 4L1ZA 4LNDA 4CMLA 4GEWA 4FPVA 3G4TA 3G00A 5J3PA 1ATND 3L1WA 1DE9A 1ZWXA 3CJCD 3I46A 5J8NA 4JG3A 5INQA 3DNIA 4CMNA 3W3DB 1DEWA 3NR8A 3FZIA 5CFGA 4F1RA 4K6LF 3G3CA 4F1HB 1HD7A 2O3CA 3MPRA
chains in the Genus database with same CATH homology


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