1DE8A

Human apurinic/apyrimidinic endonuclease-1 (ape1) bound to abasic dna
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
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 [corrected
pubmed doi rcsb
molecule tags Lyase/dna
source organism Homo sapiens
molecule keywords DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)-3')
total genus 83
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 1de8A00
3G2CA 3TEBA 3MTCA 5DV4A 5INNA 4F1HA 2V0RA 3G1KA 4FVAA 4F1HB 4L21A 4CMNA 3GA6A 1HD7A 2F1NA 3G38A 3G3CA 3NR8A 4RUWA 5J3PA 5INQA 5J3SA 5DFHA 4F1IA 2VOAA 2A42B 5DFIA 3MPRA 4L1ZA 3I48A 4L20A 1WDUA 4L1YA 4CMLA 2JC5A 4B5IA 4GZ2A 2V0SA 3CJCD 3G0RA 5J3ZA 1SI6X 2O3HA 5A7JA 1VYBA 1ATND 3G8VA 2UYRX 3DNIA 3FZIA 5CFGA 5DV2A 5INKA 3G00A 1E9NA 5INMA 4AWNA 2D1KB 3W2XA 2DNJA 4FPVA 1Y21A 1NTFA 1BIXA 4B5FA 2O3CA 4B5HA 2DDTA 4A9CA 4PUQA 5DFJA 3I5VA 1I9YA 1I9ZA 4F1RA 2A3ZB 4GZ0A 1YJHA 3NGQA 3I41A 5HT2A 4C1RA 3G3YA 3W3DB 3G2DA 4B5GA 4GZ1A 3G91A 3L1WA 4QHEA 2F2FB 1DE9A 2A41B 3NGNA 3N9VA 3K55A 2J63A 4GYZA 2DDSA 5J8NA 4JG3A 5INLA 3U8UA 4GEWA 3G4TA 3G6SA 3W2YA 5DG0A 1DE8A 2XSWA 3WCXA 4QH9A 2DDRA 4LNDA 1AKOA 3I46A 5EWTA 1ZWXA 2EI9A 3NGOA 4QHDA 1DEWA 3G0AA 2A40B 2ISIA 4B5JA 5J42A 5DFFA 5CFEA 2JC4A 4IEMA 2IMQX 4B5MA 4K6LF 1DNKA 1SR4B 5INOA 5INPA 5A7IA
chains in the Genus database with same CATH superfamily
3G2CA 3TEBA 3MTCA 5DV4A 5INNA 4F1HA 2V0RA 3G1KA 4FVAA 4F1HB 4L21A 4CMNA 3GA6A 1HD7A 2F1NA 3G38A 3G3CA 3NR8A 4RUWA 5J3PA 5INQA 5J3SA 5DFHA 4F1IA 2VOAA 2A42B 5DFIA 3MPRA 4L1ZA 3I48A 4L20A 1WDUA 4L1YA 4CMLA 2JC5A 4B5IA 4GZ2A 2V0SA 3CJCD 3G0RA 5J3ZA 1SI6X 2O3HA 5A7JA 1VYBA 1ATND 3G8VA 2UYRX 3DNIA 3FZIA 5CFGA 5DV2A 5INKA 3G00A 1E9NA 5INMA 4AWNA 2D1KB 3W2XA 2DNJA 4FPVA 1Y21A 1NTFA 1BIXA 4B5FA 2O3CA 4B5HA 2DDTA 4A9CA 4PUQA 5DFJA 3I5VA 1I9YA 1I9ZA 4F1RA 2A3ZB 4GZ0A 1YJHA 3NGQA 3I41A 5HT2A 4C1RA 3G3YA 3W3DB 3G2DA 4B5GA 4GZ1A 3G91A 3L1WA 4QHEA 2F2FB 1DE9A 2A41B 3NGNA 3N9VA 3K55A 2J63A 4GYZA 2DDSA 5J8NA 4JG3A 5INLA 3U8UA 4GEWA 3G4TA 3G6SA 3W2YA 5DG0A 1DE8A 2XSWA 3WCXA 4QH9A 2DDRA 4LNDA 1AKOA 3I46A 5EWTA 1ZWXA 2EI9A 3NGOA 4QHDA 1DEWA 3G0AA 2A40B 2ISIA 4B5JA 5J42A 5DFFA 5CFEA 2JC4A 4IEMA 2IMQX 4B5MA 4K6LF 1DNKA 1SR4B 5INOA 5INPA 5A7IA
chains in the Genus database with same CATH topology
3G2CA 3TEBA 3MTCA 5DV4A 5INNA 4F1HA 2V0RA 3G1KA 4FVAA 4F1HB 4L21A 4CMNA 3GA6A 1HD7A 2F1NA 3G38A 3G3CA 3NR8A 4RUWA 5J3PA 5INQA 5J3SA 5DFHA 4F1IA 2VOAA 2A42B 5DFIA 3MPRA 4L1ZA 3I48A 4L20A 1WDUA 4L1YA 4CMLA 2JC5A 4B5IA 4GZ2A 2V0SA 3CJCD 3G0RA 5J3ZA 1SI6X 2O3HA 5A7JA 1VYBA 1ATND 3G8VA 2UYRX 3DNIA 3FZIA 5CFGA 5DV2A 5INKA 3G00A 1E9NA 5INMA 4AWNA 2D1KB 3W2XA 2DNJA 4FPVA 1Y21A 1NTFA 1BIXA 4B5FA 2O3CA 4B5HA 2DDTA 4A9CA 4PUQA 5DFJA 3I5VA 1I9YA 1I9ZA 4F1RA 2A3ZB 4GZ0A 1YJHA 3NGQA 3I41A 5HT2A 4C1RA 3G3YA 3W3DB 3G2DA 4B5GA 4GZ1A 3G91A 3L1WA 4QHEA 2F2FB 1DE9A 2A41B 3NGNA 3N9VA 3K55A 2J63A 4GYZA 2DDSA 5J8NA 4JG3A 5INLA 3U8UA 4GEWA 3G4TA 3G6SA 3W2YA 5DG0A 1DE8A 2XSWA 3WCXA 4QH9A 2DDRA 4LNDA 1AKOA 3I46A 5EWTA 1ZWXA 2EI9A 3NGOA 4QHDA 1DEWA 3G0AA 2A40B 2ISIA 4B5JA 5J42A 5DFFA 5CFEA 2JC4A 4IEMA 2IMQX 4B5MA 4K6LF 1DNKA 1SR4B 5INOA 5INPA 5A7IA
chains in the Genus database with same CATH homology


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